New Tool addition: Haltools #7488
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| name: haltools | ||||||
| owner: iuc | ||||||
| description: A set of tools to for manipulating HAL alignment files | ||||||
| long_description: | | ||||||
| A set of tools to for manipulating HAL alignment files | ||||||
| homepage_url: https://github.com/ComparativeGenomicsToolkit/hal | ||||||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools | ||||||
| categories: | ||||||
| - Sequence Analysis | ||||||
| auto_tool_repositories: | ||||||
| name_template: "{{ tool_id }}" | ||||||
| description_template: "Wrapper for hal tool suite: {{ tool_name }}" | ||||||
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| description_template: "Wrapper for hal tool suite: {{ tool_name }}" | |
| description_template: "Wrapper for haltools suite: {{ tool_name }}" |
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| <tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0"> | ||||||||||
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| <tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0"> | |
| <tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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Define a PROFILE token in macros.xml
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| <tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0"> | |
| <tool id="hal_halstats" name="halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0"> |
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| <description>retrieves basic statistics from a hal file</description> | |
| <description>retrieve basic statistics from a HAL file</description> |
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| <expand macro="params_inputFormat"/> | |
| <expand macro="hal_backend_format"/> |
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| <param name="option" type="select" label="Select a print option" refresh_on_change="true" | |
| <param name="option" type="select" label="Select a print option" |
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Maybe specify an example and considering defining a sanitizer
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| <data name="out_file_csv" format="tabular" from_work_dir="stats.csv" label="${tool.name} on ${on_string}: CSV Stats"> | |
| <data name="out_file_csv" format="csv" from_work_dir="stats.csv" label="${tool.name} on ${on_string}: CSV Stats"> |
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Please extend your test for other parameters.
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Some other help text would be benefits
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| <macros> | ||||||||||||||
| <xml name="requirements"> | ||||||||||||||
| <requirements> | ||||||||||||||
| <requirement type="package" version="@TOOL_VERSION@">cactus</requirement> | ||||||||||||||
| </requirements> | ||||||||||||||
| </xml> | ||||||||||||||
| <token name="@TOOL_VERSION@">2.9.9</token> | ||||||||||||||
| <token name="@VERSION_SUFFIX@">0</token> | ||||||||||||||
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| <xml name="in_hal_file"> | ||||||||||||||
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| <xml name="in_hal_file"> | |
| <xml name="input_hal"> |
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Maybe we can skip this
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conditional not required here
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Not needed, will be taken care by TPV rule
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| <citation type="bibtex"> | |
| @misc{githubhal, | |
| title = {HAL GitHub page}, | |
| url = {https://github.com/ComparativeGenomicsToolkit/hal}, | |
| } | |
| </citation> |
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| FromGenome, ToGenome, sitesCovered1Times, sitesCovered2Times, sitesCovered3Times, sitesCovered4Times, sitesCovered5Times | ||
| Genome_1, Genome_1, 5472, 4688, 3516, 2637, 1465 | ||
| Genome_2, Genome_1, 4688, 2637, 2637, 1172, 0 | ||
| Genome_3, Genome_1, 4688, 4688, 3516, 2960, 880 | ||
| Genome_1, Genome_2, 3516, 3516, 2344, 1465, 293 | ||
| Genome_2, Genome_2, 4270, 2930, 2930, 1172, 0 | ||
| Genome_3, Genome_2, 3516, 3516, 2344, 1788, 176 | ||
| Genome_1, Genome_3, 4725, 4725, 3553, 2381, 1348 | ||
| Genome_2, Genome_3, 4725, 2791, 2791, 1033, 0 | ||
| Genome_3, Genome_3, 6139, 4725, 3553, 3136, 880 |
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