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comparison combine_metaphlan2_humann2.xml @ 0:b9809b6ee179 draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author bebatut
date Tue, 12 Apr 2016 02:55:42 -0400
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1 <tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0">
2 <description>to relate genus/species abundances and gene families/pathways abundances</description>
3
4 <requirements>
5 </requirements>
6
7 <stdio>
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 </stdio>
11
12 <version_command></version_command>
13
14 <command><![CDATA[
15 python $__tool_directory__/combine_metaphlan2_humann2.py
16 --metaphlan2_file $metaphlan2_file
17 --humann2_file $humann2_file
18 --type $type
19
20 #if str($type) == 'gene_families'
21 --output_file $gene_families_output_file
22 #else
23 --output_file $pathway_output_file
24 #end if
25 ]]></command>
26
27 <inputs>
28 <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/>
29
30 <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/>
31
32 <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)">
33 <option value="gene_families" selected="true">Gene families</option>
34 <option value="pathways">Pathways</option>
35 </param>
36 </inputs>
37
38 <outputs>
39 <data name="gene_families_output_file" format="tabular"
40 label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" >
41 <filter>type=="gene_families"</filter>
42 </data>
43 <data name="pathway_output_file" format="tabular"
44 label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" >
45 <filter>type=="pathways"</filter>
46 </data>
47 </outputs>
48
49 <tests>
50 </tests>
51
52 <help><![CDATA[
53 **What it does**
54
55 This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs to get, for each gene families/pathways and the corresponding taxonomic stratification, relative abundance of this gene family/pathway and the relative abundance of corresponding species and genus.
56 ]]></help>
57
58 <citations>
59 </citations>
60 </tool>