annotate humann2_regroup_table.xml @ 0:3d6f37e7e3a8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty
author bebatut
date Thu, 26 May 2016 10:20:59 -0400
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1 <tool id="humann2_regroup_table" name="Regroup" version="0.6.1">
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2 <description> a HUMAnN2 generated table by features</description>
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3
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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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7
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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_regroup_table --version
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14 ]]>
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15 </version_command>
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16
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17 <command><![CDATA[
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18 humann2_regroup_table
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19 -i $input_table
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20 -o $output_table
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21 --function $function
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22
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23 #if $built_in.built_in_test == "true":
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24 --groups $built_in.groups
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25 #else:
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26 --custom $built_in.file
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27 $built_in.reversed
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28 #end if
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29 ]]></command>
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30
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31 <inputs>
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32 <param name="input_table" type="data" format="tsv" label="Gene/pathway table" help="(-i)"/>
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33
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34 <param name="function" type="select" label="How to combine grouped features?" help="(--function)">
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35 <option value="sum" selected="true">Sum</option>
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36 <option value="mean">Mean</option>
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37 </param>
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38
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39 <conditional name="built_in">
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40 <param name='built_in_test' type='select' label="Use built-in grouping options?" help="">
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41 <option value="true" selected="true">Yes</option>
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42 <option value="false">No</option>
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43 </param>
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44
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45 <when value="true">
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46 <param name="groups" type="select" label="Grouping options" help="(--groups)">
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47 <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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48 <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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49 <option value="uniref50_ko">Collapses UniRef50 gene families into KEGG Orthogroups (KOs) (associations inferred from UniProt)</option>
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50 <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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51 </param>
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52 </when>
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53
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54 <when value="false">
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55 <param name="file" type="data" format="tsv" label="Custom groups file" help="(--custom)"/>
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56 <param name='reversed' type='boolean' checked="false" truevalue='--reversed' falsevalue='' label="Is the groups file reversed?" help="Mapping from features to groups. (--reversed)"/>
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57 </when>
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58 </conditional>
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59 </inputs>
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60
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61 <outputs>
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62 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" />
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="input_table" value="expected_gene_family_abundance.tsv"/>
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68 <param name="function" value="sum"/>
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69 <param name="built_in_test" value="true"/>
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70 <param name="groups" value="uniref50_ec"/>
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71 <output name="output_table" file="regrouped_gene_families_to_ec.tsv"/>
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72 </test>
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73 <test>
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74 <param name="input_table" value="expected_gene_family_abundance.tsv"/>
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75 <param name="function" value="mean"/>
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76 <param name="built_in_test" value="true"/>
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77 <param name="groups" value="uniref50_ko"/>
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78 <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/>
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79 </test>
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80 </tests>
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81
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82 <help><![CDATA[
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83 **What it does**
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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 Regroup HUMAnN2 table features is a tool for regrouping table features (abundances or coverage) given a table of feature values and a mapping of groups to component features. It produces a new table with group values in place of feature values.
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88 ]]></help>
3d6f37e7e3a8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty
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89
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90 <expand macro="citations"/>
3d6f37e7e3a8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty
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91 </tool>