Mercurial > repos > iuc > humann_unpack_pathways
comparison humann_unpack_pathways.xml @ 0:c3d043160f09 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
| author | iuc |
|---|---|
| date | Wed, 12 May 2021 09:07:12 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:c3d043160f09 |
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| 1 <tool id="humann_unpack_pathways" name="Unpack pathway abundances" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description>to show the genes for each</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="edam_ontology"/> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="version"/> | |
| 9 <command detect_errors="exit_code"><![CDATA[ | |
| 10 humann_unpack_pathways | |
| 11 --input-genes '$input_genes' | |
| 12 --input-pathways '$input_pathways' | |
| 13 #if $gene_mapping | |
| 14 --gene-mapping '$gene_mapping' | |
| 15 #end if | |
| 16 #if $pathway_mapping | |
| 17 --pathway-mapping '$pathway_mapping' | |
| 18 #end if | |
| 19 $remove_taxonomy | |
| 20 --output '$output' | |
| 21 ]]></command> | |
| 22 <inputs> | |
| 23 <param argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/> | |
| 24 <param argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/> | |
| 25 <param argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/> | |
| 26 <param argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/> | |
| 27 <param argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/> | |
| 28 </inputs> | |
| 29 <outputs> | |
| 30 <data format="tabular" name="output"/> | |
| 31 </outputs> | |
| 32 <tests> | |
| 33 <test expect_num_outputs="1"> | |
| 34 <param name="input_genes" value="demo_genefamilies.tsv"/> | |
| 35 <param name="input_pathways" value="demo_pathabundance.tsv"/> | |
| 36 <param name="remove_taxonomy" value=""/> | |
| 37 <output name="output" ftype="tabular"> | |
| 38 <assert_contents> | |
| 39 <has_text text="humann_Abundance"/> | |
| 40 <has_text text="PWY-4203|unclassified|UniRef90_Q6XMI3"/> | |
| 41 <has_n_columns n="2"/> | |
| 42 </assert_contents> | |
| 43 </output> | |
| 44 </test> | |
| 45 <test expect_num_outputs="1"> | |
| 46 <param name="input_genes" value="demo_genefamilies.tsv"/> | |
| 47 <param name="input_pathways" value="demo_pathabundance.tsv"/> | |
| 48 <param name="remove_taxonomy" value="--remove-taxonomy"/> | |
| 49 <output name="output" ftype="tabular"> | |
| 50 <assert_contents> | |
| 51 <has_text text="humann_Abundance"/> | |
| 52 <has_text text="PWY-4203|UniRef90_Q6XMI3"/> | |
| 53 <has_n_columns n="2"/> | |
| 54 </assert_contents> | |
| 55 </output> | |
| 56 </test> | |
| 57 </tests> | |
| 58 <help><![CDATA[ | |
| 59 @HELP_HEADER@ | |
| 60 | |
| 61 This tool unpacks the pathways to show the genes for each. | |
| 62 | |
| 63 It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances. | |
| 64 ]]></help> | |
| 65 <expand macro="citations"/> | |
| 66 </tool> |