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add Psortb (#1735)
* add Psortb * Update tools/psortb/psortb.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/psortb/.shed.yml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update remote repository URL for psortb tool * Update remote repository URL to use 'master' branch --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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‎tools/psortb/.shed.yml‎

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name: psortb
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owner: bgruening
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description: PSORTb — protein subcellular localization prediction for prokaryotes
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long_description: |
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Galaxy wrapper for PSORTb, a tool that predicts the subcellular
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localization of bacterial and archaeal proteins. The tool supports
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Gram-positive, Gram-negative, and Archaea models.
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homepage_url: https://psort.org/
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remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/psortb
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type: unrestricted
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categories:
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- Proteomics
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- Sequence Analysis
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‎tools/psortb/psortb.xml‎

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<tool id="psortb" name="PSORTb" version="3.0.6" profile="24.0">
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<description>Protein subcellular localization prediction for prokaryotes</description>
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<xrefs>
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<xref type="bio.tools">psortb</xref>
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</xrefs>
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<requirements>
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<container type="docker">quay.io/galaxy/psortb-cli:3.0.6</container>
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</requirements>
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<command detect_errors="exit_code">
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<![CDATA[
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mkdir \$TMPDIR/results &&
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/usr/local/psortb/bin/psort
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$gram.gram_choice
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#if $cutoff
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-c $cutoff
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#end if
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#if $divergent
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-d $divergent
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#end if
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-f fasta
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$exact
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-o $output_format
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-i $input_fasta
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&&
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mv \$TMPDIR/results/*_psortb_*.txt $output
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]]>
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</command>
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<inputs>
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<param name="input_fasta" type="data" format="fasta" label="Protein sequences (FASTA)" help="Submit protein sequences in FASTA format."/>
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<section name="gram" title="Organism classification" expanded="true">
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<param name="gram_choice" type="select" label="Organism type">
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<option value="--positive" selected="true">Gram-positive (Bacteria)</option>
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<option value="--negative">Gram-negative (Bacteria)</option>
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<option value="--archaea">Archaea</option>
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</param>
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</section>
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<param name="output_format" type="select" label="Output format" help="Choose PSORTb output format.">
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<option value="normal">Normal (human-readable)</option>
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<option value="terse">3-column (terse)</option>
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<option value="long" selected="true">30-column (long)</option>
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</param>
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<param argument="--exact" type="boolean" truevalue="--exact" falsevalue="" checked="false" label="Skip SCLBLASTe" help="Useful for batch runs of data against itself in SCLBLAST"/>
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<param argument="--cutoff" type="float" optional="true" label="Prediction cutoff" help="Sets a cutoff value for reported results (default: 7.5 used internally)."/>
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<param argument="--divergent" type="float" optional="true" label="Multiple localization cutoff" help="Sets a cutoff for flagging potential multiple localization sites."/>
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</inputs>
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<outputs>
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<data name="output" format="txt" label="PSORTb results on ${on_string}"/>
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</outputs>
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<tests>
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<test expect_num_outputs="1">
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<param name="input_fasta" value="psortb_pos.fa"/>
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<param name="gram|gram_choice" value="--positive"/>
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<param name="output_format" value="normal"/>
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<output name="output" value="psortb_pos_output.txt"/>
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</test>
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<test expect_num_outputs="1">
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<param name="input_fasta" value="psortb_neg.fa"/>
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<param name="gram|gram_choice" value="--negative"/>
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<param name="output_format" value="terse"/>
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<output name="output">
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<assert_contents>
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<has_text_matching expression="SeqID\tLocalization\tScore" />
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<has_text_matching expression="NP_949347\.1 \tUnknown\t7\.0" />
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</assert_contents>
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</output>
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</test>
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<test expect_num_outputs="1">
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<param name="input_fasta" value="psortb_arch.fa"/>
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<param name="gram|gram_choice" value="--archaea"/>
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<param name="output_format" value="long"/>
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<output name="output">
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<assert_contents>
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<has_text_matching expression="SeqID\s+CMSVM_a_Localization\s+CMSVM_a_Details\s+CWSVM_a_Localization\s+CWSVM_a_Details\s+CytoSVM_a_Localization\s+CytoSVM_a_Details\s+ECSVM_a_Localization\s+ECSVM_a_Details\s+ModHMM_a_Localization\s+ModHMM_a_Details\s+Motif_a_Localization\s+Motif_a_Details\s+Profile_a_Localization\s+Profile_a_Details\s+SCL-BLAST_a_Localization\s+SCL-BLAST_a_Details\s+SCL-BLASTe_a_Localization\s+SCL-BLASTe_a_Details\s+Signal_a_Localization\s+Signal_a_Details\s+Cytoplasmic_Score\s+CytoplasmicMembrane_Score\s+Cellwall_Score\s+Extracellular_Score\s+Final_Localization\s+Final_Localization_Details\s+Final_Score\s+Secondary_Localization\s+PSortb_Version" />
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<has_text_matching expression="YP_001689002\.1\s+Unknown\s+Unknown\s+Unknown\s+Extracellular\s+Unknown\s+1 internal helix found\s+Unknown\s+No motifs found\s+Unknown\s+No matches to profiles found\s+Extracellular\s+matched 47117675: Flagellin B1 precursor\s+Unknown\s+No matches against database\s+Unknown\s+No signal peptide detected\s+0.01\s+0.00\s+0.02\s+9.97\s+Extracellular\s+9.97\s+Flagellar\s+PSORTb version" />
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</assert_contents>
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</output>
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</test>
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</tests>
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<help>
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<![CDATA[
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PSORTb predicts the subcellular localization of bacterial and archaeal proteins.
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Input requirements
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- Protein sequences in FASTA format. All sequences in one run should belong to the same organism class.
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Options
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- Organism type: select Gram-positive (`--positive`), Gram-negative (`--negative`), or Archaea (`--archaea`).
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- Output format: `normal` (human-readable), `terse` (tab-delimited), or `long` (tab-delimited with module details).
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- Cutoff (`-c`): threshold for final localization assignment (documentation suggests ~7.5).
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- Multiple localization cutoff (`-d`): threshold to flag possible multiple localization sites.
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- Exact (`--exact`): skip SCL-BLASTe step.
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Notes
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- PSORTb emphasizes precision; proteins with ambiguous signals may be reported as Unknown.
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- Long format includes module outputs and localization scores; terse/long are suitable for bulk processing.
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Reference
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https://psort.org/documentation/index.html
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]]>
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</help>
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<citations>
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<citation type="doi">10.1093/bioinformatics/btq249</citation>
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</citations>
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</tool>

‎tools/psortb/test-data/psortb_arch.fa‎

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>YP_001689002.1
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MFEFITDEDERGQVGIGTLIVFIAMVLVAAIAAGVLINTAGYLQSKGSATGEEASAQVSNRINIVSAYGNVNNEKVDYVNLTVRQAAGADNINLTKSTIQWIGPDRATTLTYSSNSPSSLGENFTTESIKGSSADVLVDQSDRIKVIMYASGVSSNLGAGDEVQLTVTTQYGSKTTYWAQVPESLKDKNA

‎tools/psortb/test-data/psortb_neg.fa‎

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>NP_949347.1
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MQGHHFGGDMSNSEAIDNTTAKLRLAQSSSLLALALLIGSAPAQAADTDWGWLAIGAPAATAQGWTGKGVVIGVVDTGIDFSHPALSGRAFDYNYGSFVAGSNHPHATHVAGIIGATDINRGMEGVAPDVRFSSMKIFTGAGGSYLGDAAVADAYDGAIGSGVRIFNNSWGSSDSIANFTSREELLAHEPLLVGAFTRAVNADAVLVWSTGNDGRSQPSWQAAAPYYIQELKANWIAVTSVGENGTIASYANACGVAKAWCLAAPGGDFNPGIYSTIPGKDYGYMSGTSMAAPYVTGATAIARQMFPKASGAQLAQIVLQTSRDIGAPGIDDVYGWGLLAVDNIVDTINPRGAALFASAAWGRFTTLSAIGNTVLDRISDLRNGRGDVVTAPLAFAG

‎tools/psortb/test-data/psortb_pos.fa‎

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>SAK_BPP42
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MLKRSLLFLTVLLLLFSFSSITNEVSASSSFDKGKYKKGDDASYFEPTGPYLMVNVTGVDGKRNELLSPRYVEFPIKPGTTLTKEKIEYYVEWALDATAYKEFRVVELDPSAKIEVTYYDKNKKKEETKSFPITEKGFVVPDLSEHIKNPGFNLITKVVIEKK

‎tools/psortb/test-data/psortb_pos_output.txt‎

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SeqID: SAK_BPP42
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Analysis Report:
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CMSVM+ Unknown [No details]
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CWSVM+ Unknown [No details]
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CytoSVM+ Unknown [No details]
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ECSVM+ Extracellular [No details]
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ModHMM+ Unknown [1 internal helix found]
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Motif+ Unknown [No motifs found]
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Profile+ Unknown [No matches to profiles found]
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SCL-BLAST+ Extracellular [matched 134189: Staphylokinase precursor (Neutral proteinase) (Protease III)]
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SCL-BLASTe+ Unknown [No matches against database]
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Signal+ Non-Cytoplasmic [Signal peptide detected]
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Localization Scores:
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Extracellular 9.98
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Cellwall 0.02
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CytoplasmicMembrane 0.00
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Cytoplasmic 0.00
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Final Prediction:
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Extracellular 9.98
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-------------------------------------------------------------------------------
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