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annotate humann2_rename_table.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_rename_table" name="Rename HUMAnN2 table features" version="0.1.0">
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2 <description></description>
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3
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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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947012405a6e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
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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_rename_table --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 humann2_rename_table
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23 -i $input_table
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24 -o $output_table
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26 --names $built_in.names
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27 $built_in.simplify
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28 -c $built_in.file
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29 ]]></command>
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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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31 <inputs>
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32 <param name="input_table" type="data" format="tsv" label="Gene/pathway
947012405a6e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
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33 table" help=""/>
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34
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35 <param name="names" type="select" label="Table features that
947012405a6e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
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36 can be renamed" help="(--names)">
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37 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
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38 <option value="metacyc-pwy">MetaCyc pathways</option>
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39 <option value="ko">KEGG Orthogroups (KO)</option>
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40 <option value="ec">Enzyme commision (EC)</option>
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41 <option value="uniref50">UniRef50 gene families</option>
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42 </param>
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43 <param name='simplify' type='boolean' checked="false" truevalue='-s'
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44 falsevalue='' label="Remove non-alphanumeric characters from names?"
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45 help="(--simplify)"/>
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46 <param name="file" type="data" format="tsv" label="Custom mapping file of feature IDs to full names" help="(--custom)"/>
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47 </inputs>
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48
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49 <outputs>
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50 <data format="tsv" name="output_table" label="Renamed table for
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51 ${on_string} (HUMAnN2)" />
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52 </outputs>
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53
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54 <tests>
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55 </tests>
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56
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57 <help><![CDATA[
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58 **What it does**
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59
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60 Rename HUMAnN2 table features is a tool for renaming table features given built-in or custom mapping.
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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 ]]></help>
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64
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65 <citations>
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66 </citations>
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67 </tool>