Mercurial > repos > bebatut > combine_metaphlan2_humann2

annotate combine_metaphlan2_humann2.xml @ 0:b9809b6ee179 draft

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author bebatut
date Tue, 12 Apr 2016 02:55:42 -0400
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b9809b6ee179 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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1 <tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0">
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2 <description>to relate genus/species abundances and gene families/pathways abundances</description>
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4 <requirements>
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5 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 </stdio>
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12 <version_command></version_command>
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14 <command><![CDATA[
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15 python $__tool_directory__/combine_metaphlan2_humann2.py
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16 --metaphlan2_file $metaphlan2_file
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17 --humann2_file $humann2_file
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18 --type $type
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20 #if str($type) == 'gene_families'
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21 --output_file $gene_families_output_file
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22 #else
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23 --output_file $pathway_output_file
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24 #end if
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25 ]]></command>
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27 <inputs>
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28 <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/>
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30 <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/>
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32 <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)">
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33 <option value="gene_families" selected="true">Gene families</option>
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34 <option value="pathways">Pathways</option>
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35 </param>
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36 </inputs>
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38 <outputs>
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39 <data name="gene_families_output_file" format="tabular"
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40 label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" >
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41 <filter>type=="gene_families"</filter>
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42 </data>
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43 <data name="pathway_output_file" format="tabular"
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44 label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" >
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45 <filter>type=="pathways"</filter>
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46 </data>
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47 </outputs>
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48
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49 <tests>
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50 </tests>
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52 <help><![CDATA[
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53 **What it does**
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54
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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.
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56 ]]></help>
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58 <citations>
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59 </citations>
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60 </tool>