Mercurial > repos > iuc > humann2_unpack_pathways

comparison humann2_unpack_pathways.xml @ 0:d2e4fee96dd1 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author iuc
date Tue, 01 Aug 2017 07:56:57 -0400
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1 <tool id="humann2_unpack_pathways" name="Unpack pathway abundances to show genes included" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>humann2_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version"/>
8 <command detect_errors="exit_code"><![CDATA[
9 humann2_unpack_pathways
10 --input-genes '$input_genes'
11 --input-pathways '$input_pathways'
12 #if $gene_mapping
13 --gene-mapping '$gene_mapping'
14 #end if
15 #if $pathway_mapping
16 --pathway-mapping '$pathway_mapping'
17 #end if
18 $remove_taxonomy
19 --output '$output'
20 ]]></command>
21 <inputs>
22 <param name="input_genes" argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/>
23 <param name="input_pathways" argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/>
24 <param name="gene_mapping" argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/>
25 <param name="pathway_mapping" argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/>
26 <param name="remove_taxonomy" argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/>
27 </inputs>
28 <outputs>
29 <data format="tsv" name="output" label="${tool.name} on ${on_string}" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input_genes" value="demo_genefamilies.tsv"/>
34 <param name="input_pathways" value="demo_pathabundance.tsv"/>
35 <param name="remove_taxonomy" value=""/>
36 <output name="output" md5="993534d3e8fea242066352a0e4d67c8a"/>
37 </test>
38 <test>
39 <param name="input_genes" value="demo_genefamilies.tsv"/>
40 <param name="input_pathways" value="demo_pathabundance.tsv"/>
41 <param name="remove_taxonomy" value="--remove-taxonomy"/>
42 <output name="output" md5="b145ce760ce656b9e3ddb00d3ff4cf46"/>
43 </test>
44 </tests>
45 <help><![CDATA[
46 @HELP_HEADER@
47
48 This utility will unpack the pathways to show the genes for each. It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances.
49 ]]></help>
50 <expand macro="citations"/>
51 </tool>