Mercurial > repos > iuc > hamronize_tool
changeset 4:cbfa52c8f1ef draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
| author | iuc |
|---|---|
| date | Tue, 05 Mar 2024 19:47:12 +0000 |
| parents | e13b801516dd |
| children | |
| files | hamronize_tool.xml macros.xml test-data/mykrobe/mykrobe.json |
| diffstat | 3 files changed, 545 insertions(+), 120 deletions(-) [+] |
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--- a/hamronize_tool.xml Fri Feb 09 21:27:18 2024 +0000 +++ b/hamronize_tool.xml Tue Mar 05 19:47:12 2024 +0000 @@ -1,166 +1,306 @@ -<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> +<tool id="hamronize_tool" name="hAMRonize" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Antimicrobial Resistance Analysis Reports into a common data structure</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements" /> <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ +#import re - <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 +#set $no_origin_info_tools = ['mykrobe', 'tbprofiler'] +#set $origin_tools = ['abricate', 'amrfinderplus', 'fargene', 'srst2', 'staramr'] +#set $in_fname_tools = ['amrfinderplus', 'amrplusplus', 'ariba', 'csstar', 'deeparg', 'fargene', 'groot', 'kmerresistance', 'pointfinder', 'resfarms', 'rgi', 'srax', 'srst2'] +#set $ref_db_name_tools = ['ariba', 'csstar', 'groot', 'srax'] +#set $input_file_name = re.sub('[^\s\w\-\.]', '_', str($input.report.element_identifier)) + +hamronize + '$input.tool' + '$input.report' + --format '$format' + --output '$output' +#if $input.tool not in $no_origin_info_tools + #if $input.tool in $origin_tools and $input.origin.origin + #if $input.origin.origin + --analysis_software_version '$input.report.tool_version' #else - --output hamronized.json - #end if - - #if $select_tool.tool in $extra_1_param - --input_file_name $select_tool.input_file_name + --analysis_software_version '$input.origin.analysis_software_version' #end if - - #if $select_tool.tool in $extra_2_params - --reference_database_id $select_tool.reference_database_id - #end if - - $report + --reference_database_version '$input.reference_database_version' + #else + --analysis_software_version '$input.analysis_software_version' + --reference_database_version '$input.reference_database_version' + #end if +#end if +#if $input.tool in $in_fname_tools + #if str($input.input_file_name) != '' + --input_file_name '$input.input_file_name' + #else + --input_file_name '$input_file_name' + #end if +#end if +#if $input.tool in $ref_db_name_tools + --reference_database_name '$input.reference_database_name' +#end if ]]> </command> - <inputs> - <param name="report" type="data" format="txt,tabular" label="Report file"/> - <conditional name="select_tool"> + <conditional name="input"> <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> + <option value="abricate" selected="true">ABRicate</option> + <option value="amrfinderplus">AMRFinderPlus</option> + <option value="amrplusplus">AMRplusplus</option> + <option value="ariba">ARIBA</option> + <option value="csstar">c-SSTAR</option> + <option value="deeparg">DeepARG</option> + <option value="fargene">fARGene</option> + <option value="groot">GROOT</option> + <option value="kmerresistance">KmerResistance</option> + <option value="mykrobe">Mykrobe</option> + <option value="pointfinder">PointFinder</option> + <option value="resfams">ResFams</option> + <option value="resfinder">ResFinder</option> + <option value="rgi">RGI</option> + <option value="srax">SraX</option> + <option value="srst2">SRST2</option> + <option value="staramr">StarAMR</option> + <option value="tbprofiler">TBProfiler</option> </param> - <when value="abricate" /> - <when value="resfinder" /> - <when value="staramr" /> + <when value="abricate"> + <expand macro="report" format="tabular" label="ABRicate Report file"/> + <expand macro="origin" software="ABRicate"/> + </when> <when value="amrfinderplus"> + <expand macro="report" format="tabular" label="AMRFinderPlus Report file"/> <expand macro="input_file_name"/> + <expand macro="origin" software="AMRFinderPlus"/> + </when> + <when value="amrplusplus"> + <expand macro="report" format="tabular" label="AMRplusplus gene report"/> + <expand macro="input_file_name"/> + <expand macro="analysis_software_version" software="AMRplusplus"/> + <expand macro="reference_database_version"/> </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="report" format="tabular" label="ARIBA output"/> <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"/> + <expand macro="analysis_software_version" software="ARIBA"/> + <expand macro="reference_database_version"/> + <expand macro="reference_database_name" software="ARIBA"/> </when> <when value="csstar"> + <expand macro="report" format="tabular" label="c-SSTAR output"/> <expand macro="input_file_name"/> - <expand macro="reference_database_id"/> + <expand macro="analysis_software_version" software="c-SSTAR" /> + <expand macro="reference_database_version"/> + <expand macro="reference_database_name" software="c-SSTAR"/> + </when> + <when value="deeparg"> + <expand macro="report" format="tabular" label="DeepARG output"/> + <expand macro="input_file_name"/> + <expand macro="analysis_software_version" software="DeepARG"/> + </when> + <when value="fargene"> + <expand macro="report" format="txt" label="fARGene HMM Search Result"/> + <expand macro="input_file_name"/> + <expand macro="origin" software="fARGene"/> </when> - <when value="amrplusplus"> + <when value="groot"> + <expand macro="report" format="tabular" label="GROOT output"/> + <expand macro="input_file_name"/> + <expand macro="analysis_software_version" software="GROOT" /> + <expand macro="reference_database_version"/> + <expand macro="reference_database_name" software="GROOT"/> + </when> + <when value="kmerresistance"> + <expand macro="report" format="tabular" label="KmerResistance gene report"/> <expand macro="input_file_name"/> + <expand macro="analysis_software_version" software="KmerResistance"/> + <expand macro="reference_database_version"/> + </when> + <when value="mykrobe"> + <expand macro="report" format="json" label="Mykrobe Report file"/> + </when> + <when value="pointfinder"> + <param name="report" type="data" format="txt" label="PointFinder results"/> + <expand macro="input_file_name"/> + <expand macro="analysis_software_version" software="PointFinder"/> + <expand macro="reference_database_version"/> </when> <when value="resfams"> + <param name="report" type="data" format="txt" label="ResFams results"/> <expand macro="input_file_name"/> + <expand macro="analysis_software_version" software="ResFams"/> + <expand macro="reference_database_version"/> + </when> + <when value="resfinder"> + <param name="report" type="data" format="tabular" label="ResFinder results"/> + <expand macro="input_file_name"/> + <expand macro="analysis_software_version" software="ResFinder"/> + <expand macro="reference_database_version"/> + </when> + <when value="rgi"> + <param name="report" type="data" format="txt" label="RGI output"/> + <expand macro="input_file_name"/> + <expand macro="analysis_software_version" software="RGI"/> + <expand macro="reference_database_version"/> </when> - <when value="groot"> + <when value="srax"> + <param name="report" type="data" format="tabular" label="SraX detected ARGs"/> <expand macro="input_file_name"/> - <expand macro="reference_database_id"/> + <expand macro="analysis_software_version" software="SraX"/> + <expand macro="reference_database_version"/> + <expand macro="reference_database_name" software="SraX"/> + </when> + <when value="srst2"> + <expand macro="report" format="tabular" label="SRST2 report"/> + <expand macro="input_file_name"/> + <expand macro="origin" software="SRST2"/> + </when> + <when value="staramr"> + <expand macro="report" format="tabular" label="StarAMR ResFinder output"/> + <expand macro="origin" software="StarAMR"/> + </when> + <when value="tbprofiler"> + <param name="report" type="data" format="tabular" label="TBProfiler output"/> </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 argument="--format" type="select" label="Output format"> + <option value="tsv" selected="True">Tabular</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 ${on_string}: Table" from_work_dir="hamronized.tsv"> - <filter>output_format == "tsv"</filter> - </data> - <data format="json" name="output_json" label="${tool.name} on ${on_string}: JSON" from_work_dir="hamronized.json"> - <filter>output_format == "json"</filter> + <data name="output" format="tabular" label="${tool.name} on ${on_string} (${input.tool})"> + <change_format> + <when input="format" value="json" format="json"/> + </change_format> </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" /> + <conditional name="input"> + <param name="tool" value="abricate" /> + <param name="report" value="abricate/report.tsv" ftype="tabular" /> + <conditional name="origin"> + <param name="origin" value="false"/> + <param name="analysis_software_version" value="tool_v_1"/> + </conditional> + <param name="reference_database_version" value="db_v_1"/> + </conditional> + <param name="format" value="tsv" /> + <output name="output" ftype="tabular"> + <assert_contents> + <has_n_lines n="8"/> + <has_n_columns n="36"/> + <has_text text="input_file_name"/> + <has_text text="GCF_010120755.1_ASM1012075v1_genomic"/> + <has_text text="vanS-M"/> + <has_text text="db_v_1"/> + </assert_contents> + </output> </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" /> + <conditional name="input"> + <param name="tool" value="abricate" /> + <param name="report" value="abricate/report.tsv" ftype="tabular" /> + <conditional name="origin"> + <param name="origin" value="false"/> + <param name="analysis_software_version" value="tool_v_1"/> + </conditional> + <param name="reference_database_version" value="db_v_1"/> + </conditional> + <param name="format" value="json" /> + <output name="output" ftype="json"> + <assert_contents> + <has_text text="input_file_name"/> + <has_text text="GCF_010120755.1_ASM1012075v1_genomic"/> + <has_text text="vanS-M"/> + <has_text text="db_v_1"/> + </assert_contents> + </output> </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" /> + <conditional name="input"> + <param name="tool" value="ariba" /> + <param name="report" value="ariba/report.tsv" ftype="tabular" /> + <param name="input_file_name" value="ariba_report" /> + <param name="analysis_software_version" value="ariba_v1" /> + <param name="reference_database_version" value="db_v_1" /> + <param name="reference_database_name" value="dbname" /> + </conditional> + <param name="format" value="tsv" /> + <output name="output" ftype="tabular"> + <assert_contents> + <has_n_lines n="257"/> + <has_n_columns n="36"/> + <has_text text="input_file_name"/> + <has_text text="ariba_report"/> + <has_text text="AAC_3__IId"/> + <has_text text="ariba_v1"/> + <has_text text="db_v_1"/> + <has_text text="dbname"/> + </assert_contents> + </output> + </test> + <!-- mykrobe --> + <test expect_num_outputs="1"> + <conditional name="input"> + <param name="tool" value="mykrobe" /> + <param name="report" value="mykrobe/mykrobe.json" ftype="json" /> + </conditional> + <param name="format" value="tsv" /> + <output name="output" ftype="tabular"> + <assert_contents> + <has_n_lines n="2"/> + <has_n_columns n="36"/> + <has_text text="input_file_name"/> + <has_text text="rpoB"/> + <has_text text="v0.10.0"/> + <has_text text="NC_000962.3"/> + <has_text text="mykrobe"/> + </assert_contents> + </output> </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"/> + <conditional name="input"> + <param name="tool" value="rgi" /> + <param name="report" value="rgi/rgi.txt" ftype="txt" /> + <param name="analysis_software_version" value="rgi_v1" /> + <param name="reference_database_version" value="card_v1" /> + </conditional> + <param name="format" value="tsv" /> + <output name="output" ftype="tabular"> + <assert_contents> + <has_n_lines n="42"/> + <has_n_columns n="36"/> + <has_text text="input_file_name"/> + <has_text text="rgi.txt"/> + <has_text text="oqxA"/> + <has_text text="CARD"/> + <has_text text="card_v1"/> + <has_text text="rgi_v1"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ **What it does** -Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure +hAMRonization parses multiple Antimicrobial Resistance Analysis Reports +from disparate antimicrobial resistance gene detection tools into a single +unified format. + +This is an implementation of the hAMRonization AMR detection specification +scheme which supports gene presence/absence resistance and mutational resistance +(if supported by the underlying tool). **Inputs** -Depends on the tools with hAMRonizable reports: +Report or output of an antimicrobial resistance gene detection tool: * abricate: abricate's output report i.e., OUTPUT.tsv * amrfinderplus: amrfinderplus's output report i.e., OUTPUT.tsv
--- a/macros.xml Fri Feb 09 21:27:18 2024 +0000 +++ b/macros.xml Tue Mar 05 19:47:12 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">1.0.3</token> - <token name="@PROFILE@">20.05</token> + <token name="@TOOL_VERSION@">1.1.4</token> + <token name="@PROFILE@">23.1</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">hamronization</xref> @@ -11,20 +11,36 @@ <requirement type="package" version="@TOOL_VERSION@">hamronization</requirement> </requirements> </xml> - <xml name="input_file_name"> - <param name="input_file_name" type="text" label="Input file name" help="Sample name which was scanned with the tool"></param> + <xml name="version_command"> + <version_command>hamronize --version</version_command> + </xml> + <xml name="report" token_format="tabular" token_label="Report" > + <param argument="report" type="data" format="@FORMAT@" label="@LABEL@"/> </xml> - <xml name="reference_database_id"> - <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id of this tool"></param> + <xml name="input_file_name"> + <param argument="--input_file_name" type="text" label="Sample name" help="If not provided, the input dataset will be taken"/> + </xml> + <xml name="analysis_software_version" token_software=""> + <param argument="--analysis_software_version" type="text" label="@SOFTWARE@ version"/> </xml> <xml name="reference_database_version"> - <param name="reference_database_version" type="text" label="Reference database version"></param> + <param name="reference_database_version" type="text" label="Reference database version"/> </xml> - <xml name="analysis_software_version"> - <param name="analysis_software_version" type="text" label="Analysis software version"></param> + <xml name="origin" token_software=""> + <conditional name="origin"> + <param name="origin" type="select" label="Input generated within Galaxy on this server without leaving it?"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"/> + <when value="false"> + <expand macro="analysis_software_version" software="@SOFTWARE@" /> + </when> + </conditional> + <expand macro="reference_database_version"/> </xml> - <xml name="version_command"> - <version_command>hamronize --version</version_command> + <xml name="reference_database_name" token_software=""> + <param name="reference_database_name" type="text" label="Reference database name for @SOFTWARE@"/> </xml> <xml name="citations"> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mykrobe/mykrobe.json Tue Mar 05 19:47:12 2024 +0000 @@ -0,0 +1,269 @@ +{ + "SRR6916544": { + "susceptibility": { + "Rifampicin": { + "predict": "r", + "called_by": { + "rpoB_S450L-TCG761154TTG": { + "variant": null, + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -3594.140082249598, + -136.57739012799902, + -2127.6812715680494 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 40, + "min_non_zero_depth": 32, + "kmer_count": 796, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 60, + "min_non_zero_depth": 58, + "kmer_count": 1150, + "klen": 20 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 3458 + }, + "_cls": "Call.VariantCall" + } + } + } + }, + "phylogenetics": { + "phylo_group": { + "Mycobacterium_tuberculosis_complex": { + "percent_coverage": 99.681, + "median_depth": 124 + } + }, + "sub_complex": { + "Unknown": { + "percent_coverage": -1, + "median_depth": -1 + } + }, + "species": { + "Mycobacterium_tuberculosis": { + "percent_coverage": 98.804, + "median_depth": 121 + } + }, + "lineage": { + "lineage": [ + "lineage2.2.10", + "lineage3" + ], + "calls_summary": { + "lineage2.2.10": { + "good_nodes": 3, + "tree_depth": 3, + "genotypes": { + "lineage2": 0.5, + "lineage2.2": 0.5, + "lineage2.2.10": 0.5 + } + }, + "lineage3": { + "good_nodes": 1, + "tree_depth": 1, + "genotypes": { + "lineage3": 0.5 + } + } + }, + "calls": { + "lineage2.2.10": { + "lineage2": { + "G497491A": { + "variant": "ref-G497491A?var_name=G497491A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G497491A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -4852.294042193726, + -68.00214340670391, + -4045.7527933854217 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 76, + "min_non_zero_depth": 70, + "kmer_count": 1498, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 85, + "min_non_zero_depth": 82, + "kmer_count": 1695, + "klen": 21 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 4784 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage2.2": { + "G2505085A": { + "variant": "ref-G2505085A?var_name=G2505085A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G2505085A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -3967.5854789566783, + -20.859193826341652, + -3054.5971617777313 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 58, + "min_non_zero_depth": 56, + "kmer_count": 1160, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 69, + "min_non_zero_depth": 64, + "kmer_count": 1383, + "klen": 21 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 3947 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage2.2.10": { + "G1364706A": { + "variant": "ref-G1364706A?var_name=G1364706A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G1364706A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -2360.5217287767423, + -145.4041778818164, + -3052.427673185898 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 51, + "min_non_zero_depth": 47, + "kmer_count": 1017, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 42, + "min_non_zero_depth": 42, + "kmer_count": 848, + "klen": 21 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 2215 + }, + "_cls": "Call.VariantCall" + } + } + }, + "lineage3": { + "lineage3": { + "C3273107A": { + "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -3093.863597972382, + -19.52878016336399, + -3761.204834296007 + ], + 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