Mercurial > repos > bebatut > humann2_join_tables

annotate humann2_join_tables.xml @ 0:e3c88925060e 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 11:40:32 -0500
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1 <tool id="humann2_join_tables" name="Join" version="@WRAPPER_VERSION@.0">
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2 <description>HUMAnN2 generated tables</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_join_tables --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 mkdir tmp_dir
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20 &&
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22 #for $table in $input_tables
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23 cp '$table.input_table' 'tmp_dir' &&
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24 #end for
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26 humann2_join_tables
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27 -i 'tmp_dir'
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28 -o '$joined_table'
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29 ]]></command>
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30
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31 <inputs>
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32 <repeat name="input_tables" title="Gene/pathway tables to join">
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33 <param name="input_table" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table" help=""/>
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34 </repeat>
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35 </inputs>
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36
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37 <outputs>
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38 <data format="tsv" name="joined_table" label="${tool.name} on ${on_string}: Joined table" />
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39 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input_tables_0|input_table" value="demo_pathabundance.tsv"/>
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44 <param name="input_tables_1|input_table" value="demo_pathcoverage.tsv"/>
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45 <output name="joined_table">
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46 <assert_contents>
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47 <has_text text="PWY490-3: nitrate reduction VI (assimilatory)|unclassified" />
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48 <has_text text="PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I" />
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49 <has_text text="VALSYN-PWY: L-valine biosynthesis" />
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50 <has_text text="UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus" />
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51 </assert_contents>
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52 </output>
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53 </test>
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54 </tests>
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55
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56 <help><![CDATA[
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57 **What it does**
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58 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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59
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60 Join HUMAnN2 tables is a tool to join gene or pathway tables of multiple samples into a single table.
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61 ]]></help>
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62
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63 <expand macro="citations"/>
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64 </tool>