Mercurial > repos > iuc > humann2_regroup_table

annotate humann2_regroup_table.xml @ 4:bd7a9c6efb10 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
author iuc
date Mon, 01 Feb 2021 18:09:51 +0000
parents 1d141730ec69
children 88ff1d78fd30
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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 <macros>
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4 <import>humann2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 humann2_regroup_table
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10 --input '$input'
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11 -o '$output_table'
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12 --function '$function'
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13 #if $built_in.built_in_test == "true":
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14 --groups '$built_in.gene_family_groups.groups'
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15 #else:
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16 --custom '$built_in.custom'
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17 $built_in.reversed
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18 #end if
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19 --precision '$precision'
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20 --ungrouped '$ungrouped'
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21 --protected '$protected'
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22 ]]></command>
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23 <inputs>
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24 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
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25 <param argument="--function" type="select" label="How to combine grouped features?">
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26 <option value="sum" selected="true">Sum</option>
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27 <option value="mean">Mean</option>
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28 </param>
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29 <conditional name="built_in">
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30 <param name="built_in_test" type="select" label="Use built-in grouping options?" help="">
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31 <option value="true" selected="true">Yes</option>
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32 <option value="false">No</option>
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33 </param>
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34 <when value="true">
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35 <conditional name="gene_family_groups">
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36 <param name="gene_family_type" type="select" label="Gene family type">
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37 <option value="uniref50">UniRef50 gene families</option>
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38 <option value="uniref90">UniRef90 gene families</option>
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39 </param>
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40 <when value="uniref50">
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41 <param name="groups" type="select" label="Grouping options" help="(--groups)">
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42 <!--<option value="uniref50_go">UniRef50 gene families into GO</option>
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43 <option value="uniref50_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
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44 <option value="uniref50_eggnog">UniRef50 gene families into eggNOG</option>
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45 <option value="uniref50_pfam">UniRef50 gene families into PFAM</option>
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46 <option value="uniref50_level4ec">UniRef50 gene families into level4ec</option>
1
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47 <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option>-->
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48 <option value="uniref50_rxn">UniRef50 gene families into metacyc reactions</option>
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49 </param>
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50 </when>
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51 <when value="uniref90">
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52 <param name="groups" type="select" label="Grouping options" help="(--groups)">
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53 <!--<option value="uniref90_go">UniRef90 gene families into GO</option>
0
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54 <option value="uniref90_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
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55 <option value="uniref90_eggnog">UniRef90 gene families into eggNOG</option>
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56 <option value="uniref90_pfam">UniRef90 gene families into PFAM</option>
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57 <option value="uniref90_level4ec">UniRef90 gene families into level4ec</option>
1
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58 <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option>-->
0
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59 <option value="uniref90_rxn">UniRef90 gene families into metacyc reactions</option>
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60 </param>
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61 </when>
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62 </conditional>
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63 </when>
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64 <when value="false">
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65 <param argument="--custom" type="data" format="tsv" label="Custom groups file"/>
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66 <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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67 </when>
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68 </conditional>
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69 <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/>
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70 <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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71 <param argument="--protected" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Carry through protected features, such as 'UNMAPPED'?"/>
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72 </inputs>
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73 <outputs>
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74 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" />
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75 </outputs>
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76 <tests>
1
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77 <!--<test>
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78 <param name="input" value="demo_genefamilies.tsv"/>
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79 <param name="function" value="sum"/>
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80 <param name="built_in_test" value="true"/>
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81 <param name="gene_family_type" value="uniref90"/>
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82 <param name="groups" value="uniref90_infogo1000"/>
1
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83 <param name="precision" value="3"/>
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84 <param name="ungrouped" value="Y"/>
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85 <param name="protected" value="Y"/>
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86 <output name="output_table" file="regrouped_gene_families_to_infogo1000.tsv"/>
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87 </test>-->
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88 <!--<test>
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89 <param name="input" value="demo_genefamilies.tsv"/>
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90 <param name="function" value="mean"/>
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91 <param name="built_in_test" value="true"/>
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92 <param name="gene_family_type" value="uniref90"/>
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93 <param name="groups" value="uniref90_ko"/>
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94 <param name="precision" value="3"/>
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95 <param name="ungrouped" value="Y"/>
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96 <param name="protected" value="Y"/>
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97 <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/>
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98 </test>-->
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99 <test>
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100 <param name="input" value="demo_genefamilies.tsv"/>
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101 <param name="function" value="sum"/>
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102 <param name="built_in_test" value="true"/>
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103 <param name="gene_family_type" value="uniref90"/>
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104 <param name="groups" value="uniref90_rxn"/>
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105 <param name="precision" value="3"/>
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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_rxn.tsv"/>
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109 </test>
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110 </tests>
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111 <help><![CDATA[
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112 @HELP_HEADER@
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113
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114 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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115 ]]></help>
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116 <expand macro="citations"/>
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117 </tool>