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Merge pull request #210 from xtrojak/137-creator-tag
general tool cleanup + creator tags
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‎tools/aplcms_to_ramclustr_converter/.shed.yml‎

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- aplcms_to_ramclustr_converter.xml
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- aplcms_to_ramclustr_converter.py
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- test-data
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- macros.xml
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homepage_url: https://github.com/RECETOX/galaxytools/
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long_description: Tool to convert parquet table from apLCMS output to csv input for RamClustR
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name: aplcms_to_ramclustr_converter

‎tools/aplcms_to_ramclustr_converter/aplcms_to_ramclustr_converter.xml‎

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<tool id="aplcms_to_ramclustr_converter" name="apLCMS to RamClustR converter" version="0.1.0+galaxy0" python_template_version="3.5">
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<description>converts apLCMS parquet output to RamClustR csv input</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="creator"/>
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<requirements>
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<requirement type="package" version="1.1.5">pandas</requirement>
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<requirement type="package" version="4.0.0">pyarrow</requirement>
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<output name="out_file" file="output.csv" ftype="csv"/>
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</test>
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</tests>
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<help><![CDATA[
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Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements.
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**Workflow position**
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- Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms>`_ Unsupervised or Hybrid
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- Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV)
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]]></help>
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<help>
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<![CDATA[
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@HELP@
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]]>
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</help>
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</tool>

‎tools/aplcms_to_ramclustr_converter/macros.xml‎

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<macros>
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<xml name="creator">
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<creator>
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<person
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givenName="Martin"
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familyName="Čech"
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url="https://github.com/martenson"
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identifier="0000-0002-9318-1781" />
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<person
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givenName="Maksym"
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familyName="Skoryk"
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url="https://github.com/maximskorik"
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identifier="0000-0003-2056-8018" />
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<organization
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url="https://www.recetox.muni.cz/"
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email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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name="RECETOX MUNI" />
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</creator>
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</xml>
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<token name="@HELP@">
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<![CDATA[
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Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements.
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**Workflow position**
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- Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms>`_ Unsupervised or Hybrid
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- Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV)
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]]>
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</token>
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</macros>

‎tools/biotransformer/biotransformer.xml‎

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<tool id="biotransformer" name="BioTransformer" version="1.1.5+galaxy1">
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<requirements>
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<requirement type="package" version="1.1.5">biotransformer</requirement>
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<requirement type="package" version="3.1.1">openbabel</requirement>
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<requirement type="package" version="1.1.1">pandas</requirement>
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<requirement type="package" version="3.7">python</requirement>
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</requirements>
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<command><![CDATA[ python3 '${__tool_directory__}/wrapper_biotransformer.py'
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-k $k
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-b $b
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-s $steps
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-t $tolerance
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-a
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-icsv $input_file
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-ocsv $output_file
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-ocsvDup $output_file2
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-ocsvDup2 $output_file3
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="creator"/>
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<requirements>
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<requirement type="package" version="1.1.5">biotransformer</requirement>
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<requirement type="package" version="3.1.1">openbabel</requirement>
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<requirement type="package" version="1.1.1">pandas</requirement>
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<requirement type="package" version="3.7">python</requirement>
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</requirements>
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<command><![CDATA[
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python3 '${__tool_directory__}/wrapper_biotransformer.py'
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-k $k
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-b $b
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-s $steps
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-t $tolerance
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-a
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-icsv $input_file
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-ocsv $output_file
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-ocsvDup $output_file2
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-ocsvDup2 $output_file3
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]]>
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</command>
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<inputs>
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<param name="k" type="select" value="pred"
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label="The task to be permed [pred=prediction, cid=compound identification].">
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<option value="pred" selected="true">pred</option>
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<option value="cid">cid</option>
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</param>
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<param name="b" type="select" value="ecbased" label="The type of description.">
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<option value="ecbased" selected="true">EC-based</option>
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<option value="cyp450">CYP450</option>
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<option value="phaseII">Phase II</option>
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<option value="hgut">Human gut microbial</option>
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<option value="superbio">Human super transformer 1 (superbio)</option>
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<option value="allHuman">Human super transformer 2 (allHuman)</option>
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<option value="envimicro">Environmental microbial</option>
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</param>
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<param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/>
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<param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/>
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<param name="input_file" type="data" format="csv" label="Input CSV file."/>
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</inputs>
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]]>
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</command>
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<inputs>
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<param name="k" type="select" value="pred" label="The task to be permed [pred=prediction, cid=compound identification].">
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<option value="pred" selected="true" >pred</option>
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<option value="cid">cid</option>
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</param>
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<param name="b" type="select" value="ecbased" label="The type of description.">
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<option value="ecbased" selected="true" >EC-based</option>
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<option value="cyp450">CYP450</option>
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<option value="phaseII">Phase II</option>
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<option value="hgut">Human gut microbial</option>
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<option value="superbio">Human super transformer 1 (superbio)</option>
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<option value="allHuman">Human super transformer 2 (allHuman)</option>
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<option value="envimicro">Environmental microbial</option>
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</param>
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<param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/>
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<param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/>
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<param name="input_file" type="data" format="csv" label="Input CSV file."/>
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</inputs>
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<outputs>
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<data format="csv" name="output_file" label="BioTransformer - output."/>
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<data format="csv" name="output_file2" label="BioTransformer - filtered CSV output."/>
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<data format="csv" name="output_file3" label="BioTransformer - super-filtered CSV output."/>
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</outputs>
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<outputs>
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<data format="csv" name="output_file" label="BioTransformer - output."/>
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<data format="csv" name="output_file2" label="BioTransformer - filtered CSV output."/>
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<data format="csv" name="output_file3" label="BioTransformer - super-filtered CSV output."/>
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</outputs>
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<tests>
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<test>
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<param name="k" value="pred"/>
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<param name="b" value="allHuman"/>
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<param name="steps" value="1"/>
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<param name="tolerance" value="0.01"/>
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<param name="input_file" value="smiles.csv"/>
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<output name="output_file" value="output1.csv"/>
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<output name="output_file2" value="output2.csv"/>
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<output name="output_file3" value="output3.csv"/>
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</test>
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</tests>
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<help>
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BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut micr obiota,
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as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification,
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based on the metabolism prediction.
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BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v2.1.
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Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and
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build upon the material under the condition that they must give appropriate credit, provide links to the license,
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and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be
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included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires
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explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer
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web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to
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acknowledge the authors.
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Parameters explanation:
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**Input.** Currently, only a CSV file with one SMILES per line is accepted.
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**The type of prediction:** EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut
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microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro).
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**The number of steps for the prediction:** this option will be used for the EC-based, CYP450, Phase II, and Environmental
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microbial biotransformers. The default value is 1.
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**Mass tolerance for metabolite identification** (default is 0.01).
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**Output of BioTransformer** with CSV as an input are 3 CSV files. One without any filtering, second with filtered
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duplicates based on 6 columns (InChI, InChIKey, Synonyms, Molecular formula, Major Isotope Mass, AlogP) and third with
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filtered duplicates based on 3 columns (Molecular formula, Major Isotope Mass, AlogP).
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(* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation
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first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable
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reaction(Oxidation, reduction, (de-)conjugation) at each step.
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</help>
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<citations>
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<citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation>
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</citations>
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<tests>
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<test>
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<param name="k" value="pred"/>
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<param name="b" value="allHuman"/>
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<param name="steps" value="1"/>
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<param name="tolerance" value="0.01"/>
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<param name="input_file" value="smiles.csv"/>
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<output name="output_file" value="output1.csv"/>
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<output name="output_file2" value="output2.csv"/>
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<output name="output_file3" value="output3.csv"/>
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</test>
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</tests>
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<help>
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<![CDATA[
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@HELP@
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]]>
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</help>
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<citations>
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<citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation>
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</citations>
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</tool>

‎tools/biotransformer/macros.xml‎

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<macros>
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<xml name="creator">
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<creator>
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<person
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givenName="Martin"
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familyName="Čech"
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url="https://github.com/martenson"
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identifier="0000-0002-9318-1781" />
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<person
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givenName="Karolína"
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familyName="Trachtová"
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url="https://github.com/trachtok" />
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<organization
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url="https://www.recetox.muni.cz/"
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email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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name="RECETOX MUNI" />
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</creator>
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</xml>
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<token name="@HELP@">
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<![CDATA[
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BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut micr obiota,
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as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification,
23+
based on the metabolism prediction.
24+
25+
BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v2.1.
26+
27+
Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and
28+
build upon the material under the condition that they must give appropriate credit, provide links to the license,
29+
and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be
30+
included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires
31+
explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer
32+
web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to
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acknowledge the authors.
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Parameters explanation:
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**Input.** Currently, only a CSV file with one SMILES per line is accepted.
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**The type of prediction:** EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut
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microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro).
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**The number of steps for the prediction:** this option will be used for the EC-based, CYP450, Phase II, and Environmental
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microbial biotransformers. The default value is 1.
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**Mass tolerance for metabolite identification** (default is 0.01).
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**Output of BioTransformer** with CSV as an input are 3 CSV files. One without any filtering, second with filtered
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duplicates based on 6 columns (InChI, InChIKey, Synonyms, Molecular formula, Major Isotope Mass, AlogP) and third with
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filtered duplicates based on 3 columns (Molecular formula, Major Isotope Mass, AlogP).
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(* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation
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first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable
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reaction(Oxidation, reduction, (de-)conjugation) at each step.
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]]>
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</token>
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</macros>

‎tools/export_to_path/export_to_path.xml‎

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<tool id="export_to_path" name="export to path" version="0.0.2">
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="creator"/>
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<description>on a filesystem accessible to compute node</description>
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<requirements>
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<requirement type="package" version="3.6">python</requirement>
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</requirements>
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<command detect_errors="aggressive"><![CDATA[
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python '$__tool_directory__/export_to_path.py'
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-p '$remote_path'
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python '$__tool_directory__/export_to_path.py'
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-p '$remote_path'
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#if $mzml_dataset
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'${mzml_dataset}' '${mzml_dataset.ext}'
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#end if
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#if $mzml_dataset
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'${mzml_dataset}' '${mzml_dataset.ext}'
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#end if
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#if $json_metadata
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'${json_metadata}' '${json_metadata.ext}'
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#end if
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#if $json_metadata
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'${json_metadata}' '${json_metadata.ext}'
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#end if
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#if $txt_metadata
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'${txt_metadata}' '${txt_metadata.ext}'
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#end if
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#if $txt_metadata
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'${txt_metadata}' '${txt_metadata.ext}'
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#end if
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> '$log'
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> '$log'
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]]></command>
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<inputs>
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<param name="mzml_dataset" type="data" format="mzml" label="mzML Dataset to export" optional="true"/>
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<param name="json_metadata" type="data" format="json" label="JSON metadata to export" optional="true"/>
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<param name="txt_metadata" type="data" format="txt" label="TXT metadata to export" optional="true"/>
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<param name="remote_path" type="text" value="" label="Remote path of the new mzML dataset." help="Full absolute path to the new mzml dataset to export.">
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<validator type="empty_field" />
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<sanitizer sanitize="false" />
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<param name="remote_path" type="text" value="" label="Remote path of the new mzML dataset."
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help="Full absolute path to the new mzml dataset to export.">
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<validator type="empty_field"/>
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<sanitizer sanitize="false"/>
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</param>
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</inputs>
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<outputs>
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<data name="log" format="txt" />
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<data name="log" format="txt"/>
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</outputs>
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<tests>
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</tests>
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<help><![CDATA[
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Simple tool to copy datasets to a directory on the cluster.
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]]></help>
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<help>
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<![CDATA[
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@HELP@
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]]>
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</help>
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<citations/>
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</tool>

‎tools/export_to_path/macros.xml‎

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<macros>
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<xml name="creator">
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<creator>
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<person
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givenName="Martin"
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familyName="Čech"
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url="https://github.com/martenson"
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identifier="0000-0002-9318-1781" />
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<person
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givenName="Maksym"
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familyName="Skoryk"
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url="https://github.com/maximskorik"
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identifier="0000-0003-2056-8018" />
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<organization
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url="https://www.recetox.muni.cz/"
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email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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name="RECETOX MUNI" />
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</creator>
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</xml>
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<token name="@HELP@">
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<![CDATA[
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Simple tool to copy datasets to a directory on the cluster.
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]]>
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</token>
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</macros>

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