Mercurial > repos > bebatut > humann2

annotate in_development/humann2_regroup_table.xml @ 5:2bf5fcf30e1f 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 08:34:43 -0500
parents 947012405a6e
children
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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_regroup_table" name="Regroup 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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10
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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_regroup_table --version
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18 ]]>
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19 </version_command>
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20
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21 <command><![CDATA[
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22 humann2_regroup_table
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23 -i $input_table
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24 -o $output_table
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25 --function $function
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26
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27 #if $built_in.test:
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28 --groups $built_in.groups
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29 #else:
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30 --custom $built_in.file
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31 $built_in.reversed
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32 #end if
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33 ]]></command>
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34
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35 <inputs>
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36 <param name="input_table" type="data" format="tsv" label="Gene/pathway
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37 table" help=""/>
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38
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39 <param name="function" type="select" label="How to combine grouped features?" help="(--function)">
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40 <option value="sum" selected="true">Sum</option>
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41 <option value="mean">Mean</option>
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42 </param>
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43
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44 <conditional name="built_in">
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45 <param name='test' type='boolean' checked="false" truevalue='true'
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46 falsevalue='false' label="Use built-in grouping options?"
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47 help=""/>
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48 <when value="true">
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49 <param name="groups" type="select" label="Grouping options" help="(--groups)">
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50 <option value="uniref50_ec" selected="true">Collapses UniRef50 gene families into top level enzyme commission (EC) categories (associations inferred from UniProt)</option>
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51 <option value="uniref50_go">Collapses UniRef50 gene families into a subset of non-redundant, high-level Gene Ontology (GO) categories (associations inferred from UniProt and a HUMAnN2-specific parsing of the GO hierarchy)</option>
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52 <option value="uniref50_ko">Collapses UniRef50 gene fammilies into KEGG Orthogroups (KOs) (associations inferred from UniProt)</option>
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53 <option value="uniref50_rxn">Collapses UniRef50 gene families into metacyc reactions (use of reaction abundances to compute the abundance and coverage of broader metabolic pathways)</option>
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54 </param>
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55 </when>
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56 <when value="false">
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57 <param name="file" type="data" format="tsv" label="Custom groups file" help="(--custom)"/>
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58 <param name='reversed' type='boolean' checked="false" truevalue='--reversed'
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59 falsevalue='' label="Is the groups file reversed?"
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60 help="Mapping from features to groups. (--reversed)"/>
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61 </when>
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62 </conditional>
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63 </inputs>
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64
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65 <outputs>
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66 <data format="tsv" name="output_table" label="Regrouped table for
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67 ${on_string} (HUMAnN2)" />
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68 </outputs>
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69
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70 <tests>
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71 <test>
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72 <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
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73 <param name="function" value="sum"/>
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74 <param name="test" value="true"/>
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75 <param name="groups" value="uniref50_ec"/>
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76 <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/>
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77 </test>
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78 </tests>
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79
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80 <help><![CDATA[
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81 **What it does**
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82
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83 Regroup HUMAnN2 table features is a tool for egrouping table features. Given a table of feature values and a mapping of groups to component features, produce a new table with group values in place of feature values.
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84
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85 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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86
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87 ]]></help>
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88
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89 <citations>
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90 </citations>
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91 </tool>