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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 7a2ad14035dc
children
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6:9152525e3c73 7:229eef1c5498
1 <tool id="humann" name="HUMAnN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="humann" name="HUMAnN" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>to profile presence/absence and abundance of microbial pathways and gene families</description> 2 <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="prescreen"> 5 <xml name="prescreen">
6 <section name="prescreen" title="Prescreen / Identifying community species" expanded="true"> 6 <section name="prescreen" title="Prescreen / Identifying community species" expanded="true">
168 <expand macro="edam_ontology"/> 168 <expand macro="edam_ontology"/>
169 <expand macro="requirements"/> 169 <expand macro="requirements"/>
170 <expand macro="version"/> 170 <expand macro="version"/>
171 <command detect_errors="exit_code"><![CDATA[ 171 <command detect_errors="exit_code"><![CDATA[
172 #import re 172 #import re
173 #if $in.input.ext.startswith("fasta") 173 #if $input_conditional.input.ext.startswith("fasta")
174 #set ext="fasta" 174 #set ext="fasta"
175 #else if $in.input.ext.startswith("fastq") 175 #else if $input_conditional.input.ext.startswith("fastq")
176 #set ext="fastq" 176 #set ext="fastq"
177 #else if $in.input.ext.endswith("bam") 177 #else if $input_conditional.input.ext.endswith("bam")
178 #set ext="bam" 178 #set ext="bam"
179 #else if $in.input.ext == 'sam' 179 #else if $input_conditional.input.ext == 'sam'
180 #set ext="sam" 180 #set ext="sam"
181 #else if $in.input.ext == 'biom1' 181 #else if $input_conditional.input.ext == 'biom1'
182 #set ext="biom" 182 #set ext="biom"
183 #else if $input_conditional.input.ext == 'tabular'
184 #set ext="genetable"
185 #else if $input_conditional.input.ext == 'tsv'
186 #set ext="genetable"
183 #else 187 #else
184 >&2 "unknown extension $in.input.ext" 188 >&2 "unknown extension $input_conditional.input.ext"
185 exit 1; 189 exit 1;
186 #end if 190 #end if
187 #if $in.input.ext.endswith(".gz") 191 #if $input_conditional.input.ext.endswith(".gz")
188 #set ext+=".gz" 192 #set ext+=".gz"
189 #end if 193 #end if
190 194
191 #if $wf.selector == 'bypass_prescreen' 195 #if $wf.selector == 'bypass_prescreen'
192 @NUCLEOTIDE_SEARCH_PREPARE@ 196 @NUCLEOTIDE_SEARCH_PREPARE@
207 @NUCLEOTIDE_SEARCH_PREPARE@ 211 @NUCLEOTIDE_SEARCH_PREPARE@
208 @TRANSLATED_SEARCH_PREPARE@ 212 @TRANSLATED_SEARCH_PREPARE@
209 #end if 213 #end if
210 214
211 humann 215 humann
212 --input '$input' 216 --input '$input_conditional.input'
213 --input-format $ext 217 --input-format $ext
214 -o 'output' 218 -o 'output'
215 #if $wf.selector == 'bypass_prescreen' 219 #if $wf.selector == 'bypass_prescreen'
216 --bypass-prescreen 220 --bypass-prescreen
217 @NUCLEOTIDE_SEARCH_RUN@ 221 @NUCLEOTIDE_SEARCH_RUN@
253 $out.remove_stratified_output 257 $out.remove_stratified_output
254 --threads "\${GALAXY_SLOTS:-4}" 258 --threads "\${GALAXY_SLOTS:-4}"
255 --memory-use minimum 259 --memory-use minimum
256 ]]></command> 260 ]]></command>
257 <inputs> 261 <inputs>
258 <conditional name="in"> 262 <conditional name="input_conditional">
259 <param name="selector" type="select" label="Input(s)"> 263 <param name="selector" type="select" label="Input(s)">
260 <option value="raw" selected="true">Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))</option> 264 <option value="raw" selected="true">Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))</option>
261 <option value="mapping">Pre-computed mappings of reads to database sequences</option> 265 <option value="mapping">Pre-computed mappings of reads to database sequences</option>
262 <option value="abundance">Pre-computed (typically gene) abundance tables</option> 266 <option value="abundance">Pre-computed (typically gene) abundance tables</option>
263 </param> 267 </param>
348 </param> 352 </param>
349 </section> 353 </section>
350 </inputs> 354 </inputs>
351 <outputs> 355 <outputs>
352 <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" > 356 <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
353 <filter>out['output_format'] == "tsv"</filter> 357 <filter>input_conditional['selector'] != "abundance" and out['output_format'] == "tsv"</filter>
354 </data> 358 </data>
355 <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance as biom"> 359 <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance as biom">
356 <filter>out['output_format'] == "biom"</filter> 360 <filter>input_conditional['selector'] != "abundance" and out['output_format'] == "biom"</filter>
357 </data> 361 </data>
358 <data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" > 362 <data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
359 <filter>out['output_format'] == "tsv"</filter> 363 <filter>out['output_format'] == "tsv"</filter>
360 </data> 364 </data>
361 <data name="pathcoverage_biom" format="biom1" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage as biom"> 365 <data name="pathcoverage_biom" format="biom1" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage as biom">
394 </data> 398 </data>
395 </outputs> 399 </outputs>
396 <tests> 400 <tests>
397 <!-- This test refers to the Metaphlan v3 DB format, and hence should fail, which is to be caught gracefully. --> 401 <!-- This test refers to the Metaphlan v3 DB format, and hence should fail, which is to be caught gracefully. -->
398 <test expect_exit_code="42" expect_failure="true"> 402 <test expect_exit_code="42" expect_failure="true">
399 <conditional name="in"> 403 <conditional name="input_conditional">
400 <!-- raw fasta file --> 404 <!-- raw fasta file -->
401 <param name="selector" value="raw"/> 405 <param name="selector" value="raw"/>
402 <param name="input" value="demo.fastq.gz"/> 406 <param name="input" value="demo.fastq.gz"/>
403 </conditional> 407 </conditional>
404 <conditional name="wf"> 408 <conditional name="wf">
425 </section> 429 </section>
426 </conditional> 430 </conditional>
427 </test> 431 </test>
428 <!-- This test refers to the Metaphlan v4 DB format, and hence should be a straight pass. --> 432 <!-- This test refers to the Metaphlan v4 DB format, and hence should be a straight pass. -->
429 <test expect_num_outputs="12"> 433 <test expect_num_outputs="12">
430 <conditional name="in"> 434 <conditional name="input_conditional">
431 <!-- raw fasta file --> 435 <!-- raw fasta file -->
432 <param name="selector" value="raw"/> 436 <param name="selector" value="raw"/>
433 <param name="input" value="demo.fastq.gz"/> 437 <param name="input" value="demo.fastq.gz"/>
434 </conditional> 438 </conditional>
435 <conditional name="wf"> 439 <conditional name="wf">
578 <has_text text=">unclassified_read000867|100"/> 582 <has_text text=">unclassified_read000867|100"/>
579 </assert_contents> 583 </assert_contents>
580 </output> 584 </output>
581 </test> 585 </test>
582 <test expect_num_outputs="4"> 586 <test expect_num_outputs="4">
583 <conditional name="in"> 587 <conditional name="input_conditional">
584 <!-- fastq file --> 588 <!-- fastq file -->
585 <param name="selector" value="raw"/> 589 <param name="selector" value="raw"/>
586 <param name="input" value="demo.fasta.gz"/> 590 <param name="input" value="demo.fasta.gz"/>
587 </conditional> 591 </conditional>
588 <conditional name="wf"> 592 <conditional name="wf">
658 <has_text text="Total gene families after translated alignment: "/> 662 <has_text text="Total gene families after translated alignment: "/>
659 </assert_contents> 663 </assert_contents>
660 </output> 664 </output>
661 </test> 665 </test>
662 <test expect_num_outputs="4"> 666 <test expect_num_outputs="4">
663 <conditional name="in"> 667 <conditional name="input_conditional">
664 <param name="selector" value="raw"/> 668 <param name="selector" value="raw"/>
665 <param name="input" value="demo.fasta.gz"/> 669 <param name="input" value="demo.fasta.gz"/>
666 </conditional> 670 </conditional>
667 <conditional name="wf"> 671 <conditional name="wf">
668 <!-- bypass_taxonomic_profiling --> 672 <!-- bypass_taxonomic_profiling -->
740 <has_text text="Total gene families after translated alignment"/> 744 <has_text text="Total gene families after translated alignment"/>
741 </assert_contents> 745 </assert_contents>
742 </output> 746 </output>
743 </test> 747 </test>
744 <test expect_num_outputs="4"> 748 <test expect_num_outputs="4">
745 <conditional name="in"> 749 <conditional name="input_conditional">
746 <!-- mapping SAM file --> 750 <!-- mapping SAM file -->
747 <param name="selector" value="mapping"/> 751 <param name="selector" value="mapping"/>
748 <param name="input" value="demo.sam"/> 752 <param name="input" value="demo.sam"/>
749 </conditional> 753 </conditional>
750 <conditional name="wf"> 754 <conditional name="wf">
812 <has_text text="Computing gene families"/> 816 <has_text text="Computing gene families"/>
813 <has_text text="Computing pathways abundance and coverage"/> 817 <has_text text="Computing pathways abundance and coverage"/>
814 </assert_contents> 818 </assert_contents>
815 </output> 819 </output>
816 </test> 820 </test>
821 <!-- Test abundance input table -->
822 <test expect_num_outputs="3">
823 <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"/>
830 <has_text text="UNINTEGRATED"/>
831 <has_text text="PWY-5423"/>
832 <has_n_columns n="2"/>
833 <has_n_lines n="8"/>
834 </assert_contents>
835 </output>
836 <output name="pathabundance_tsv" ftype="tabular">
837 <assert_contents>
838 <has_text text="UNMAPPED"/>
839 <has_text text="UNINTEGRATED"/>
840 <has_text text="PWY-5423"/>
841 <has_n_columns n="2"/>
842 <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>
817 <test expect_num_outputs="4"> 853 <test expect_num_outputs="4">
818 <conditional name="in"> 854 <conditional name="input_conditional">
819 <!-- raw fasta file --> 855 <!-- raw fasta file -->
820 <param name="selector" value="raw"/> 856 <param name="selector" value="raw"/>
821 <param name="input" value="demo.fastq.gz"/> 857 <param name="input" value="demo.fastq.gz"/>
822 </conditional> 858 </conditional>
823 <conditional name="wf"> 859 <conditional name="wf">
878 <has_text text="Total gene families"/> 914 <has_text text="Total gene families"/>
879 </assert_contents> 915 </assert_contents>
880 </output> 916 </output>
881 </test> 917 </test>
882 <test expect_num_outputs="4"> 918 <test expect_num_outputs="4">
883 <conditional name="in"> 919 <conditional name="input_conditional">
884 <!-- raw fasta file --> 920 <!-- raw fasta file -->
885 <param name="selector" value="raw"/> 921 <param name="selector" value="raw"/>
886 <param name="input" value="demo.fastq.gz"/> 922 <param name="input" value="demo.fastq.gz"/>
887 </conditional> 923 </conditional>
888 <conditional name="wf"> 924 <conditional name="wf">
954 </assert_contents> 990 </assert_contents>
955 </output> 991 </output>
956 </test> 992 </test>
957 <!-- This test should fail for as metaphlan v4 is invoked on outdated input DB. --> 993 <!-- This test should fail for as metaphlan v4 is invoked on outdated input DB. -->
958 <test expect_exit_code="1" expect_failure="true"> 994 <test expect_exit_code="1" expect_failure="true">
959 <conditional name="in"> 995 <conditional name="input_conditional">
960 <!-- raw fasta file --> 996 <!-- raw fasta file -->
961 <param name="selector" value="raw"/> 997 <param name="selector" value="raw"/>
962 <param name="input" value="demo.fastq.gz"/> 998 <param name="input" value="demo.fastq.gz"/>
963 </conditional> 999 </conditional>
964 <conditional name="wf"> 1000 <conditional name="wf">