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Merge pull request #7650 from RZ9082/humann
Humann - Add missing extension
2 parents 7bf2bea + 9b1acc2 commit f434c09

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Lines changed: 56 additions & 20 deletions

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‎tools/humann/humann.xml‎

Lines changed: 56 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<tool id="humann" name="HUMAnN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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<tool id="humann" name="HUMAnN" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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<description>to profile presence/absence and abundance of microbial pathways and gene families</description>
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<macros>
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<import>macros.xml</import>
@@ -170,21 +170,25 @@
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<expand macro="version"/>
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<command detect_errors="exit_code"><![CDATA[
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#import re
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#if $in.input.ext.startswith("fasta")
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#if $input_conditional.input.ext.startswith("fasta")
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#set ext="fasta"
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#else if $in.input.ext.startswith("fastq")
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#else if $input_conditional.input.ext.startswith("fastq")
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#set ext="fastq"
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#else if $in.input.ext.endswith("bam")
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#else if $input_conditional.input.ext.endswith("bam")
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#set ext="bam"
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#else if $in.input.ext == 'sam'
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#else if $input_conditional.input.ext == 'sam'
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#set ext="sam"
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#else if $in.input.ext == 'biom1'
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#else if $input_conditional.input.ext == 'biom1'
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#set ext="biom"
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#else if $input_conditional.input.ext == 'tabular'
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#set ext="genetable"
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#else if $input_conditional.input.ext == 'tsv'
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#set ext="genetable"
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#else
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>&2 "unknown extension $in.input.ext"
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>&2 "unknown extension $input_conditional.input.ext"
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exit 1;
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#end if
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#if $in.input.ext.endswith(".gz")
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#if $input_conditional.input.ext.endswith(".gz")
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#set ext+=".gz"
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#end if
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@@ -209,7 +213,7 @@
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#end if
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humann
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--input '$input'
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--input '$input_conditional.input'
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--input-format $ext
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-o 'output'
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#if $wf.selector == 'bypass_prescreen'
@@ -255,7 +259,7 @@ humann
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--memory-use minimum
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]]></command>
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<inputs>
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<conditional name="in">
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<conditional name="input_conditional">
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<param name="selector" type="select" label="Input(s)">
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<option value="raw" selected="true">Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))</option>
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<option value="mapping">Pre-computed mappings of reads to database sequences</option>
@@ -350,10 +354,10 @@ humann
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</inputs>
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<outputs>
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<data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
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<filter>out['output_format'] == "tsv"</filter>
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<filter>input_conditional['selector'] != "abundance" and out['output_format'] == "tsv"</filter>
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</data>
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<data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance as biom">
356-
<filter>out['output_format'] == "biom"</filter>
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<filter>input_conditional['selector'] != "abundance" and out['output_format'] == "biom"</filter>
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</data>
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<data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
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<filter>out['output_format'] == "tsv"</filter>
@@ -396,7 +400,7 @@ humann
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<tests>
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<!-- This test refers to the Metaphlan v3 DB format, and hence should fail, which is to be caught gracefully. -->
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<test expect_exit_code="42" expect_failure="true">
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<conditional name="in">
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<conditional name="input_conditional">
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<!-- raw fasta file -->
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<param name="selector" value="raw"/>
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<param name="input" value="demo.fastq.gz"/>
@@ -427,7 +431,7 @@ humann
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</test>
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<!-- This test refers to the Metaphlan v4 DB format, and hence should be a straight pass. -->
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<test expect_num_outputs="12">
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<conditional name="in">
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<conditional name="input_conditional">
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<!-- raw fasta file -->
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<param name="selector" value="raw"/>
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<param name="input" value="demo.fastq.gz"/>
@@ -580,7 +584,7 @@ humann
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</output>
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</test>
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<test expect_num_outputs="4">
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<conditional name="in">
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<conditional name="input_conditional">
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<!-- fastq file -->
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<param name="selector" value="raw"/>
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<param name="input" value="demo.fasta.gz"/>
@@ -660,7 +664,7 @@ humann
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</output>
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</test>
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<test expect_num_outputs="4">
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<conditional name="in">
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<conditional name="input_conditional">
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<param name="selector" value="raw"/>
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<param name="input" value="demo.fasta.gz"/>
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</conditional>
@@ -742,7 +746,7 @@ humann
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</output>
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</test>
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<test expect_num_outputs="4">
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<conditional name="in">
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<conditional name="input_conditional">
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<!-- mapping SAM file -->
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<param name="selector" value="mapping"/>
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<param name="input" value="demo.sam"/>
@@ -814,8 +818,40 @@ humann
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</assert_contents>
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</output>
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</test>
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<!-- Test abundance input table -->
822+
<test expect_num_outputs="3">
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<conditional name="input_conditional">
824+
<param name="selector" value="abundance"/>
825+
<param name="input" value="demo_genefamilies.tsv"/>
826+
</conditional>
827+
<output name="pathcoverage_tsv" ftype="tabular">
828+
<assert_contents>
829+
<has_text text="UNMAPPED"/>
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<has_text text="UNINTEGRATED"/>
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<has_text text="PWY-5423"/>
832+
<has_n_columns n="2"/>
833+
<has_n_lines n="8"/>
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</assert_contents>
835+
</output>
836+
<output name="pathabundance_tsv" ftype="tabular">
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<assert_contents>
838+
<has_text text="UNMAPPED"/>
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<has_text text="UNINTEGRATED"/>
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<has_text text="PWY-5423"/>
841+
<has_n_columns n="2"/>
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<has_n_lines n="8"/>
843+
</assert_contents>
844+
</output>
845+
<output name="log" ftype="txt">
846+
<assert_contents>
847+
<has_text text="processing gene table"/>
848+
<has_text text="g__Bacteroides.s__Bacteroides_vulgatus"/>
849+
<has_text text="computing pathways"/>
850+
</assert_contents>
851+
</output>
852+
</test>
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<test expect_num_outputs="4">
818-
<conditional name="in">
854+
<conditional name="input_conditional">
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<!-- raw fasta file -->
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<param name="selector" value="raw"/>
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<param name="input" value="demo.fastq.gz"/>
@@ -880,7 +916,7 @@ humann
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</output>
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</test>
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<test expect_num_outputs="4">
883-
<conditional name="in">
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<conditional name="input_conditional">
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<!-- raw fasta file -->
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<param name="selector" value="raw"/>
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<param name="input" value="demo.fastq.gz"/>
@@ -956,7 +992,7 @@ humann
956992
</test>
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<!-- This test should fail for as metaphlan v4 is invoked on outdated input DB. -->
958994
<test expect_exit_code="1" expect_failure="true">
959-
<conditional name="in">
995+
<conditional name="input_conditional">
960996
<!-- raw fasta file -->
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<param name="selector" value="raw"/>
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<param name="input" value="demo.fastq.gz"/>

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