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view cooc_pubmut.xml @ 2:0349d8981030 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 43a520ebfbf379e815fb2397da6bbf360666e385
author | iuc |
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date | Mon, 02 Oct 2023 19:59:31 +0000 |
parents | f193fef5b19d |
children | ce8b15a55bbe |
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<tool id="cooc_pubmut" name="Cojac: pubmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> pretty-prints cojac mutbamscan co-occurrence results </description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools"/> <expand macro="requirements"> <requirement type="package" version="3.1.3">pandoc</requirement> <requirement type="package" version="6.2.1">gmp</requirement> </expand> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ #if $annotations.availability == 'full': #set $voc_config = $annotations.voc_source @VOCDIR_COMMAND@ #end if cojac cooc-pubmut #if $annotations.availability == 'full': -m voc/ #end if #if $annotations.availability != 'none': -a '$annotations.in_amp' #end if #if $cooc_data.ext == 'json': -j '$cooc_data' #else -y '$cooc_data' #end if -q #if $out_opts.format == 'tsv': -o cooc-table.tsv #else: -o cooc-table.csv #if $out_opts.format == 'html': && pandoc cooc-table.csv -o cooc-table.html #end if #end if ]]></command> <inputs> <param name="cooc_data" type="data" format="json,yaml" label="Co-occurrence results generated by mutbamscan" help="The tool can work with json- or yaml-formatted output of cojac mutbamscan."/> <conditional name="annotations"> <param name="availability" type="select" label="Available amplicon and lineage annotations" help="For best readability of its report the tool requires a per-lineage amplicon info dataset (in yaml format) produced by the mutbamscan tool and the original lineage definitions. If all you have is the per-lineage amplicon info, you can use it to obtain a nearly identical report, but cojac-internal lineage identifiers won't be translated into standard lineage names. With no available annotations a limited report can still be generated, but this is not recommended."> <option value="full">per-lineage amplicon info and original lineage definitions</option> <option value="amplicon">per-lineage amplicon info only</option> <option value="none">no annotations</option> </param> <when value="full"> <param name="in_amp" type="data" format="yaml" label="Combined cojac per-amplicon lineage definitions"/> <expand macro="vocdir_input"/> </when> <when value="amplicon"> <param name="in_amp" type="data" format="yaml" label="Combined per-amplicon lineage definitions"/> </when> <when value="none" /> </conditional> <section name="out_opts" title="Output formatting" expanded="true"> <param name="format" type="select" label="Type of output to produce"> <option value="tsv">Tab-separated (TSV)</option> <option value="csv">Comma-separated (CSV)</option> <option value="html">HTML (for display in browsers)</option> </param> </section> </inputs> <outputs> <data name="table_tsv" format="tsv" label="${tool.name} on ${on_string}: Mutation co-occurrence (TSV table)" from_work_dir="cooc-table.tsv"> <filter>out_opts['format'] == 'tsv'</filter> </data> <data name="table_csv" format="csv" label="${tool.name} on ${on_string}: Mutation co-occurrence (CSV table)" from_work_dir="cooc-table.csv"> <filter>out_opts['format'] == 'csv'</filter> </data> <data name="table_html" format="html" label="${tool.name} on ${on_string}: Mutation co-occurrence (HTML)" from_work_dir="cooc-table.html"> <filter>out_opts['format'] == 'html'</filter> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="cooc_data" value="cooc-test111.json"/> <conditional name="annotations"> <conditional name="vocdir_option"> <param name="choice" value="custom"/> <param name="voc_file" value="omicron_ba1_mutations.yaml"/> </conditional> <param name="in_amp" value="amplicons111.yaml"/> </conditional> <output name="table_tsv" ftype="tsv"> <assert_contents> <has_text text="Amplicon 76"/> <has_text text="Amplicon 81"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="cooc_data" value="cooc-test111.json"/> <conditional name="annotations"> <conditional name="vocdir_option"> <param name="choice" value="custom"/> <param name="voc_file" value="omicron_ba1_mutations.yaml"/> </conditional> <param name="in_amp" value="amplicons111.yaml"/> </conditional> <section name="out_opts"> <param name="format" value="csv"/> </section> <output name="table_csv" ftype="csv"> <assert_contents> <has_text text="Amplicon 76"/> <has_text text="Amplicon 81"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="cooc_data" value="cooc-test111.json"/> <conditional name="annotations"> <conditional name="vocdir_option"> <param name="choice" value="custom"/> <param name="voc_file" value="omicron_ba1_mutations.yaml"/> </conditional> <param name="in_amp" value="amplicons111.yaml"/> </conditional> <section name="out_opts"> <param name="format" value="html"/> </section> <output name="table_html" ftype="html"> <assert_contents> <has_text text="Amplicon 76"/> <has_text text="Amplicon 81"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_HEADER@ Information about **cojac cooc-pubmut** ======================================= The tool pretty-prints json or yaml output of cojac cooc-mutbamscan. Hint: The output (unless you select html format) is best viewed in spreadsheet software that understands linebreaks. ]]></help> <expand macro="citations"/> </tool>