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annotate humann2_join_tables.xml @ 3:ddc59d42d17c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit e5b8f29dde45dddcda6ee283212dd1bdde487f87-dirty
author bebatut
date Fri, 18 Dec 2015 04:28:22 -0500
parents 947012405a6e
children 0d3d44f13122
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947012405a6e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
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1 <tool id="humann2_join_tables" name="Join HUMAnN2 table" version="0.1.0">
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2 <description></description>
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4 <requirements>
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5 <requirement type="package" version="2.2.4">bowtie2</requirement>
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6 <requirement type="package" version="2.0">metaphlan2</requirement>
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7 <requirement type="package" version="0.6.13">diamond</requirement>
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8 <requirement type="package" version="2.0">humann2</requirement>
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9 </requirements>
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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15 <version_command>
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16 <![CDATA[
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17 humann2_join_tables --version
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18 ]]>
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19 </version_command>
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21 <command><![CDATA[
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22 `mkdir tmp_dir`
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23 &&
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25 #for $file in $input_files
947012405a6e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
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26 `cp $file tmp_dir`
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27 #end for
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947012405a6e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
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29 &&
947012405a6e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
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30 humann2_join_tables
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31 -i "tmp_dir"
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32 -o $joined_table
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33 ]]></command>
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35 <inputs>
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36 <param name="input_files" type="data" format="tsv,biom" multiple="true"
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37 label="Gene/pathway tables"
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38 help=""/>
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39 </inputs>
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41 <outputs>
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42 <data format="tsv,biom" name="joined_table" label="Joined table for
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43 ${on_string} (HUMAnN2)" />
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44 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input_files" value="humann2_sam_pathcoverage.tsv,humann2_fasta_pathcoverage.tsv"/>
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49 <output name="joined_table" file="humann2_sam_fasta_joined_pathcoverage.tsv"/>
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50 </test>
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51 </tests>
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52
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53 <help><![CDATA[
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54 **What it does**
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56 Join HUMAnN2 tables is a tool to join gene, pathway, or taxonomy tables of multiple samples in a single table.
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57
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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 ]]></help>
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61 <citations>
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62 </citations>
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63 </tool>