Mercurial > repos > thanhlv > humann_unpack_pathways

comparison humann_unpack_pathways.xml @ 0:f050021a4263 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
author thanhlv
date Mon, 13 Feb 2023 16:20:36 +0000
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1 <tool id="humann_unpack_pathways" name="Unpack pathway abundances" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
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>