Mercurial > repos > iuc > hamronize_tool
view hamronize_tool.xml @ 1:ec82fac4eb4b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
author | iuc |
---|---|
date | Sat, 23 Oct 2021 21:38:09 +0000 |
parents | d2590ecc4189 |
children | e13b801516dd |
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<tool id="hamronize_tool" name="hamronize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description> parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ #set $extra_2_params = str("ariba,srax,csstar,groot").split(",") #set $extra_1_param = $extra_2_params + str("amrfinderplus,rgi,resfinder4,deeparg,kmerresistance,srst2,amrplusplus,resfarms").split(",") hamronize ${select_tool.tool} --analysis_software_version '${analysis_software_version}' --reference_database_version '${reference_database_version}' --format ${output_format} #if $output_format == "tsv" --output hamronized.tsv #else --output hamronized.json #end if #if $select_tool.tool in $extra_1_param --input_file_name $select_tool.input_file_name #end if #if $select_tool.tool in $extra_2_params --reference_database_id $select_tool.reference_database_id #end if $report ]]> </command> <inputs> <param name="report" type="data" format="txt,tabular" label="Report file"/> <conditional name="select_tool"> <param name="tool" type="select" label="Tool"> <option value="abricate" selected="true">abricate</option> <option value="amrfinderplus">amrfinderplus</option> <option value="ariba">ariba</option> <option value="rgi">rgi</option> <option value="resfinder">resfinder</option> <option value="resfinder4">resfinder4</option> <option value="srax">srax</option> <option value="deeparg">deeparg</option> <option value="kmerresistance">kmerresistance</option> <option value="srst2">srst2</option> <option value="staramr">staramr</option> <option value="csstar">csstar</option> <option value="amrplusplus">amrplusplus</option> <option value="resfams">resfams</option> <option value="groot">groot</option> </param> <when value="abricate" /> <when value="resfinder" /> <when value="staramr" /> <when value="amrfinderplus"> <expand macro="input_file_name"/> </when> <when value="ariba"> <expand macro="input_file_name"/> <expand macro="reference_database_id"/> </when> <when value="rgi"> <expand macro="input_file_name"/> </when> <when value="resfinder4"> <expand macro="input_file_name"/> </when> <when value="srax"> <expand macro="input_file_name"/> <expand macro="reference_database_id"/> </when> <when value="deeparg"> <expand macro="input_file_name"/> </when> <when value="kmerresistance"> <expand macro="input_file_name"/> </when> <when value="srst2"> <expand macro="input_file_name"/> </when> <when value="csstar"> <expand macro="input_file_name"/> <expand macro="reference_database_id"/> </when> <when value="amrplusplus"> <expand macro="input_file_name"/> </when> <when value="resfams"> <expand macro="input_file_name"/> </when> <when value="groot"> <expand macro="input_file_name"/> <expand macro="reference_database_id"/> </when> </conditional> <param name="output_format" type="select" label="Output format" multiple="false" display="radio"> <option value="tsv" selected="True">tsv</option> <option value="json">json</option> </param> <param name="analysis_software_version" type="text" label="Analysis software version"></param> <param name="reference_database_version" type="text" label="Reference database version"></param> </inputs> <outputs> <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv"> <filter>output_format == "tsv"</filter> </data> <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json"> <filter>output_format == "json"</filter> </data> </outputs> <tests> <!-- abricate --> <test expect_num_outputs="1"> <param name="report" value="abricate/report.tsv" ftype="tabular" /> <param name="tool" value="abricate" /> <param name="output_format" value="tsv" /> <param name="reference_database_version" value="db_v_1" /> <param name="analysis_software_version" value="tool_v_1" /> <output name="output_tsv" file="hamronized_abricate.tsv" ftype="tabular" /> </test> <test expect_num_outputs="1"> <param name="report" value="abricate/report.tsv" ftype="tabular" /> <param name="tool" value="abricate" /> <param name="output_format" value="json" /> <param name="reference_database_version" value="db_v_1" /> <param name="analysis_software_version" value="tool_v_1" /> <output name="output_json" file="hamronized_abricate.json" ftype="json" /> </test> <!-- ariba --> <test expect_num_outputs="1"> <param name="report" value="ariba/report.tsv" ftype="tabular" /> <param name="tool" value="ariba" /> <param name="output_format" value="tsv" /> <param name="reference_database_version" value="db_v_1" /> <param name="analysis_software_version" value="ariba_v1" /> <param name="input_file_name" value="ariba_report" /> <param name="reference_database_id" value="dbname" /> <output name="output_tsv" file="hamronized_ariba.tsv" ftype="tabular" /> </test> <!-- rgi --> <test expect_num_outputs="1"> <param name="report" value="rgi/rgi.txt" ftype="txt" /> <param name="tool" value="rgi" /> <param name="output_format" value="tsv" /> <param name="reference_database_version" value="card_v1" /> <param name="analysis_software_version" value="rgi_v1" /> <param name="input_file_name" value="rgi_report" /> <output name="output_tsv" file="hamronized_rgi.tsv" ftype="tabular"/> </test> </tests> <help><![CDATA[ **What it does** Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure **Inputs** :: Tools with hAMRonizable reports: {abricate,amrfinderplus,ariba,rgi,resfinder,resfinder4,srax,deeparg,kmerresistance,srst2,staramr,csstar,amrplusplus,resfams,groot} abricate hAMRonize abricate's output report i.e., OUTPUT.tsv amrfinderplus hAMRonize amrfinderplus's output report i.e., OUTPUT.tsv ariba hAMRonize ariba's output report i.e., OUTDIR/OUTPUT.tsv rgi hAMRonize rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt resfinder hAMRonize resfinder's output report i.e., data_resfinder.json resfinder4 hAMRonize resfinder4's tabular output report i.e., ResFinder_results_tab.txt srax hAMRonize srax's output report i.e., sraX_detected_ARGs.tsv deeparg hAMRonize deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG kmerresistance hAMRonize kmerresistance's output report i.e., OUTPUT.KmerRes srst2 hAMRonize srst2's output report i.e., OUTPUT_srst2_report.tsv staramr hAMRonize staramr's output report i.e., resfinder.tsv csstar hAMRonize csstar's output report i.e., OUTPUT.tsv amrplusplus hAMRonize amrplusplus's output report i.e., gene.tsv resfams hAMRonize resfams's output report i.e., resfams.tblout groot hAMRonize groot's output report i.e., OUTPUT.tsv (from `groot report`) :: More: https://github.com/pha4ge/hAMRonization/#usage ]]> </help> </tool>