Mercurial > repos > bebatut > humann2_split_table

annotate humann2_split_table.xml @ 0:36a78e81ee4c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
author bebatut
date Mon, 20 Feb 2017 11:33:12 -0500
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36a78e81ee4c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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1 <tool id="humann2_split_table" name="Split" version="@WRAPPER_VERSION@.0">
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2 <description> a HUMAnN2 generated table</description>
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4 <macros>
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5 <import>humann2_macros.xml</import>
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6 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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11 <version_command>
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12 <![CDATA[
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13 humann2_split_table --version
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14 ]]>
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15 </version_command>
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17 <command><![CDATA[
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18 humann2_split_table
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19 --input '$input'
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20 -o 'output'
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21 #if $taxonomy_index
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22 --taxonomy_index '$taxonomy_index'
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23 #end if
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24 #if $taxonomy_level
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25 --taxonomy_level '$taxonomy_level'
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26 #end if
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27 ]]></command>
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28
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29 <inputs>
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30 <param argument="--input" type="data" format="tsv,biom" label="Gene table to split"/>
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31 <param argument="--taxonomy_index" type="text" label="Index of the gene in the taxonomy data" optional="true"/>
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32 <param argument="--taxonomy_level" type="select" label="Level of taxonomy for the output" optional="true" help="if input is from picrust metagenome_contributions.py">
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33 <option value="Kingdom">Kingdom</option>
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34 <option value="Phylum">Phylum</option>
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35 <option value="Class">Class</option>
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36 <option value="Order">Order</option>
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37 <option value="Family">Family</option>
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38 <option value="Genus">Genus</option>
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39 <option value="Species">Species</option>
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40 </param>
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41 </inputs>
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42
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43 <outputs>
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44 <collection type="list" name="split_tables" label="${tool.name} on ${on_string}: Split tables">
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45 <discover_datasets pattern="__designation_and_ext__" directory="output"/>
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46 </collection>
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <param name="input" value="joined_pathway_coverage_abundance.tsv"/>
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52 <output_collection name="split_tables" type="list" >
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53 <element name="demo_Coverage" file="demo_Coverage.tsv" />
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54 <element name="demo_Abundance" file="demo_Abundance.tsv" />
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55 </output_collection>
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56 </test>
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57 </tests>
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58
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59 <help><![CDATA[
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60 **What it does**
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61
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62 HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
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63
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64 Split HUMAnN2 table is a tool to split a gene table with multiple columns. This file can have been generated with the join table tool.
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65 ]]></help>
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66
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67 <expand macro="citations"/>
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68 </tool>