Mercurial > repos > bebatut > humann2_regroup_table

annotate humann2_regroup_table.xml @ 0:1271ea9b43b6 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 11:27:57 -0500
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1271ea9b43b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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1 <tool id="humann2_regroup_table" name="Regroup" version="@WRAPPER_VERSION@.0">
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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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10
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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 --input '$input'
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20 -o '$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.gene_family_groups.groups'
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25 #else:
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26 --custom '$built_in.custom'
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27 $built_in.reversed
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28 #end if
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29
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30 --ungrouped '$ungrouped'
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31 --protected '$protected'
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32 ]]></command>
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33
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34 <inputs>
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35 <param argument="--input" type="data" format="tsv" label="Gene/pathway table"/>
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36 <param argument="--function" type="select" label="How to combine grouped features?">
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37 <option value="sum" selected="true">Sum</option>
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38 <option value="mean">Mean</option>
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39 </param>
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40 <conditional name="built_in">
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41 <param name='built_in_test' type='select' label="Use built-in grouping options?" help="">
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42 <option value="true" selected="true">Yes</option>
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43 <option value="false">No</option>
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44 </param>
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45 <when value="true">
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46 <conditional name="gene_family_groups">
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47 <param name="gene_family_type" type="select" label="Gene family type">
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48 <option value="uniref50">UniRef50 gene families</option>
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49 <option value="uniref90">UniRef90 gene families</option>
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50 </param>
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51 <when value="uniref50">
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52 <param name="groups" type="select" label="Grouping options" help="(--groups)">
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53 <option value="uniref50_go">UniRef50 gene families into GO</option>
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54 <option value="uniref50_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
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55 <option value="uniref50_eggnog">UniRef50 gene families into eggNOG</option>
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56 <option value="uniref50_pfam">UniRef50 gene families into PFAM</option>
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57 <option value="uniref50_level4ec">UniRef50 gene families into level4ec</option>
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58 <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option>
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59 <option value="uniref50_rxn">UniRef50 gene families into metacyc reactions</option>
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60 </param>
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61 </when>
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62 <when value="uniref90">
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63 <param name="groups" type="select" label="Grouping options" help="(--groups)">
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64 <option value="uniref90_go">UniRef90 gene families into GO</option>
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65 <option value="uniref90_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
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66 <option value="uniref90_eggnog">UniRef90 gene families into eggNOG</option>
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67 <option value="uniref90_pfam">UniRef90 gene families into PFAM</option>
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68 <option value="uniref90_level4ec">UniRef90 gene families into level4ec</option>
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69 <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option>
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70 <option value="uniref90_rxn">UniRef90 gene families into metacyc reactions</option>
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71 </param>
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72 </when>
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73 </conditional>
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74 </when>
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75 <when value="false">
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76 <param argument="--custom" type="data" format="tsv" label="Custom groups file"/>
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77 <param argument='--reversed' type='boolean' checked="false" truevalue='--reversed' falsevalue='' label="Is the groups file reversed?" help="Mapping from features to groups"/>
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78 </when>
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79 </conditional>
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80 <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/>
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81 <param argument="--ungrouped" type='boolean' checked="true" truevalue='Y' falsevalue='N' label="Include an 'UNGROUPED' group to capture features that did not belong to other groups?"/>
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82 <param argument="--protected" type='boolean' checked="true" truevalue='Y' falsevalue='N' label="Carry through protected features, such as 'UNMAPPED'?"/>
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83 </inputs>
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84
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85 <outputs>
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86 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" />
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87 </outputs>
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88
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89 <tests>
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90 <test>
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91 <param name="input" value="demo_genefamilies.tsv"/>
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92 <param name="function" value="sum"/>
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93 <param name="built_in_test" value="true"/>
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94 <param name="gene_family_type" value="uniref90"/>
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95 <param name="groups" value="uniref90_infogo1000"/>
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96 <param name="ungrouped" value="Y"/>
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97 <param name="protected" value="Y"/>
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98 <output name="output_table" file="regrouped_gene_families_to_infogo1000.tsv"/>
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99 </test>
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100 <test>
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101 <param name="input" value="demo_genefamilies.tsv"/>
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102 <param name="function" value="mean"/>
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103 <param name="built_in_test" value="true"/>
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104 <param name="gene_family_type" value="uniref90"/>
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105 <param name="groups" value="uniref90_ko"/>
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106 <param name="ungrouped" value="Y"/>
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107 <param name="protected" value="Y"/>
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108 <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/>
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109 </test>
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110 <test>
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111 <param name="input" value="demo_genefamilies.tsv"/>
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112 <param name="function" value="sum"/>
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113 <param name="built_in_test" value="true"/>
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114 <param name="gene_family_type" value="uniref90"/>
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115 <param name="groups" value="uniref90_rxn"/>
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116 <param name="ungrouped" value="Y"/>
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117 <param name="protected" value="Y"/>
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118 <output name="output_table" file="regrouped_gene_families_to_rxn.tsv"/>
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119 </test>
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120 </tests>
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121
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122 <help><![CDATA[
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123 **What it does**
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124
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125 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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126
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127 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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128 ]]></help>
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129
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130 <expand macro="citations"/>
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131 </tool>