Mercurial > repos > iuc > humann
changeset 7:229eef1c5498 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann commit f434c096f244d1ff01a3e439bfdf8ef3999d75af
| author | iuc |
|---|---|
| date | Wed, 04 Feb 2026 17:29:49 +0000 |
| parents | 9152525e3c73 |
| children | |
| files | humann.xml |
| diffstat | 1 files changed, 56 insertions(+), 20 deletions(-) [+] |
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--- a/humann.xml Fri Sep 27 09:57:04 2024 +0000 +++ b/humann.xml Wed Feb 04 17:29:49 2026 +0000 @@ -1,4 +1,4 @@ -<tool id="humann" name="HUMAnN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> +<tool id="humann" name="HUMAnN" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>to profile presence/absence and abundance of microbial pathways and gene families</description> <macros> <import>macros.xml</import> @@ -170,21 +170,25 @@ <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ #import re -#if $in.input.ext.startswith("fasta") +#if $input_conditional.input.ext.startswith("fasta") #set ext="fasta" -#else if $in.input.ext.startswith("fastq") +#else if $input_conditional.input.ext.startswith("fastq") #set ext="fastq" -#else if $in.input.ext.endswith("bam") +#else if $input_conditional.input.ext.endswith("bam") #set ext="bam" -#else if $in.input.ext == 'sam' +#else if $input_conditional.input.ext == 'sam' #set ext="sam" -#else if $in.input.ext == 'biom1' +#else if $input_conditional.input.ext == 'biom1' #set ext="biom" +#else if $input_conditional.input.ext == 'tabular' + #set ext="genetable" +#else if $input_conditional.input.ext == 'tsv' + #set ext="genetable" #else - >&2 "unknown extension $in.input.ext" + >&2 "unknown extension $input_conditional.input.ext" exit 1; #end if -#if $in.input.ext.endswith(".gz") +#if $input_conditional.input.ext.endswith(".gz") #set ext+=".gz" #end if @@ -209,7 +213,7 @@ #end if humann - --input '$input' + --input '$input_conditional.input' --input-format $ext -o 'output' #if $wf.selector == 'bypass_prescreen' @@ -255,7 +259,7 @@ --memory-use minimum ]]></command> <inputs> - <conditional name="in"> + <conditional name="input_conditional"> <param name="selector" type="select" label="Input(s)"> <option value="raw" selected="true">Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))</option> <option value="mapping">Pre-computed mappings of reads to database sequences</option> @@ -350,10 +354,10 @@ </inputs> <outputs> <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" > - <filter>out['output_format'] == "tsv"</filter> + <filter>input_conditional['selector'] != "abundance" and out['output_format'] == "tsv"</filter> </data> <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance as biom"> - <filter>out['output_format'] == "biom"</filter> + <filter>input_conditional['selector'] != "abundance" and out['output_format'] == "biom"</filter> </data> <data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" > <filter>out['output_format'] == "tsv"</filter> @@ -396,7 +400,7 @@ <tests> <!-- This test refers to the Metaphlan v3 DB format, and hence should fail, which is to be caught gracefully. --> <test expect_exit_code="42" expect_failure="true"> - <conditional name="in"> + <conditional name="input_conditional"> <!-- raw fasta file --> <param name="selector" value="raw"/> <param name="input" value="demo.fastq.gz"/> @@ -427,7 +431,7 @@ </test> <!-- This test refers to the Metaphlan v4 DB format, and hence should be a straight pass. --> <test expect_num_outputs="12"> - <conditional name="in"> + <conditional name="input_conditional"> <!-- raw fasta file --> <param name="selector" value="raw"/> <param name="input" value="demo.fastq.gz"/> @@ -580,7 +584,7 @@ </output> </test> <test expect_num_outputs="4"> - <conditional name="in"> + <conditional name="input_conditional"> <!-- fastq file --> <param name="selector" value="raw"/> <param name="input" value="demo.fasta.gz"/> @@ -660,7 +664,7 @@ </output> </test> <test expect_num_outputs="4"> - <conditional name="in"> + <conditional name="input_conditional"> <param name="selector" value="raw"/> <param name="input" value="demo.fasta.gz"/> </conditional> @@ -742,7 +746,7 @@ </output> </test> <test expect_num_outputs="4"> - <conditional name="in"> + <conditional name="input_conditional"> <!-- mapping SAM file --> <param name="selector" value="mapping"/> <param name="input" value="demo.sam"/> @@ -814,8 +818,40 @@ </assert_contents> </output> </test> + <!-- Test abundance input table --> + <test expect_num_outputs="3"> + <conditional name="input_conditional"> + <param name="selector" value="abundance"/> + <param name="input" value="demo_genefamilies.tsv"/> + </conditional> + <output name="pathcoverage_tsv" ftype="tabular"> + <assert_contents> + <has_text text="UNMAPPED"/> + <has_text text="UNINTEGRATED"/> + <has_text text="PWY-5423"/> + <has_n_columns n="2"/> + <has_n_lines n="8"/> + </assert_contents> + </output> + <output name="pathabundance_tsv" ftype="tabular"> + <assert_contents> + <has_text text="UNMAPPED"/> + <has_text text="UNINTEGRATED"/> + <has_text text="PWY-5423"/> + <has_n_columns n="2"/> + <has_n_lines n="8"/> + </assert_contents> + </output> + <output name="log" ftype="txt"> + <assert_contents> + <has_text text="processing gene table"/> + <has_text text="g__Bacteroides.s__Bacteroides_vulgatus"/> + <has_text text="computing pathways"/> + </assert_contents> + </output> + </test> <test expect_num_outputs="4"> - <conditional name="in"> + <conditional name="input_conditional"> <!-- raw fasta file --> <param name="selector" value="raw"/> <param name="input" value="demo.fastq.gz"/> @@ -880,7 +916,7 @@ </output> </test> <test expect_num_outputs="4"> - <conditional name="in"> + <conditional name="input_conditional"> <!-- raw fasta file --> <param name="selector" value="raw"/> <param name="input" value="demo.fastq.gz"/> @@ -956,7 +992,7 @@ </test> <!-- This test should fail for as metaphlan v4 is invoked on outdated input DB. --> <test expect_exit_code="1" expect_failure="true"> - <conditional name="in"> + <conditional name="input_conditional"> <!-- raw fasta file --> <param name="selector" value="raw"/> <param name="input" value="demo.fastq.gz"/>