Mercurial > repos > iuc > humann_regroup_table

annotate humann_regroup_table.xml @ 4:31c6d107e7a5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0a3abeca0535457ddf39c394001d61cd2e45afdd
author iuc
date Mon, 24 Apr 2023 18:56:38 +0000
parents 26ce946f4da9
children
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26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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1 <tool id="humann_regroup_table" name="Regroup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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2 <description>HUMAnN table features</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam_ontology"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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10 humann_regroup_table
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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11 --input '$input'
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12 --output '$output'
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13 --function '$function'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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14 #if $grouping.type == "standard"
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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15 --groups '$grouping.groups'
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16 #else if $grouping.type == "large"
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17 --custom '$grouping.grouping.fields.path'
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18 $grouping.reversed
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19 #else:
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20 --custom '$grouping.custom'
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21 $grouping.reversed
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22 #end if
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23 --precision $precision
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24 --ungrouped '$ungrouped'
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25 --protected '$protected'
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26 ]]></command>
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27 <inputs>
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28 <param argument="--input" type="data" format="tsv,tabular" label="Gene families table"/>
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29 <param argument="--function" type="select" label="How to combine grouped features?">
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30 <option value="sum" selected="true">Sum</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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31 <option value="mean">Mean</option>
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32 </param>
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33 <conditional name="grouping">
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34 <param name="type" type="select" label="Grouping">
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35 <option value="standard">Basic grouping (to MetaCyc pathways)</option>
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36 <option value="large">Grouping with larger mapping</option>
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37 <option value="custom">Grouping with custom mapping</option>
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38 </param>
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39 <when value="standard">
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40 <param argument="--groups" type="select" label="Grouping">
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41 <option value="uniref90_rxn">UniRef90 to MetaCyc pathways</option>
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42 <option value="uniref50_rxn">UniRef50 to MetaCyc pathways</option>
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43 </param>
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44 </when>
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45 <when value="large">
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46 <param name="grouping" type="select" label="Mapping to use for the grouping">
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47 <options from_data_table="humann_utility_mapping">
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48 <validator message="No utility mapping is available" type="no_options" />
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49 <filter type="regexp" column="0" value=".*map.*(?!_name)" keep="true"/>
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50 </options>
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51 </param>
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52 <param argument="--reversed" type="boolean" checked="false" truevalue="--reversed" falsevalue="" label="Mapping from features to groups?"/>
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53 </when>
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54 <when value="custom">
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55 <param argument="--custom" type="data" format="tsv,txt,tabular" label="Custom mapping file for grouping" help="The format is explained in the help"/>
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56 <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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57 </when>
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58 </conditional>
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59 <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/>
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60 <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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61 <param argument="--protected" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Carry through protected features, such as 'UNMAPPED'?"/>
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62 </inputs>
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63 <outputs>
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64 <data name="output" format="tabular"/>
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65 </outputs>
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66 <tests>
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67 <test expect_num_outputs="1">
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68 <param name="input" value="demo_genefamilies.tsv"/>
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69 <param name="function" value="sum"/>
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70 <conditional name="grouping">
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71 <param name="type" value="standard"/>
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72 <param name="groups" value="uniref90_rxn"/>
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73 </conditional>
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74 <param name="precision" value="3"/>
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75 <param name="ungrouped" value="Y"/>
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76 <param name="protected" value="Y"/>
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77 <output name="output" ftype="tabular">
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78 <assert_contents>
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79 <has_text text="2.5.1.19-RXN|g__Bacteroides.s__Bacteroides_vulgatus"/>
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80 <has_text text="ACETYLGLUTKIN-RXN|g__Bacteroides.s__Bacteroides_vulgatus"/>
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81 </assert_contents>
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82 </output>
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83 </test>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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84 <test expect_num_outputs="1">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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85 <param name="input" value="demo_genefamilies.tsv"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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86 <param name="function" value="mean"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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parents:
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87 <conditional name="grouping">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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88 <param name="type" value="large"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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89 <param name="grouping" value="utility_mapping-full-map_go_uniref90-3.0.0-29042021"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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90 </conditional>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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91 <param name="precision" value="3"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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92 <param name="ungrouped" value="Y"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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93 <param name="protected" value="Y"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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94 <output name="output" ftype="tabular">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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95 <assert_contents>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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96 <has_text text="GO:0000049|g__Bacteroides.s__Bacteroides_vulgatus" />
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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97 <has_text text="GO:0003866|g__Bacteroides.s__Bacteroides_vulgatus" />
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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98 </assert_contents>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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99 </output>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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100 </test>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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101 <test expect_num_outputs="1">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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102 <param name="input" value="demo_genefamilies.tsv"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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103 <param name="function" value="sum"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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104 <conditional name="grouping">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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105 <param name="type" value="custom"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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106 <!-- file generated using customizemapping file -->
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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107 <param name="custom" value="test-db/utility_mapping/map_go_uniref90.txt"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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108 </conditional>
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109 <param name="precision" value="3"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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110 <param name="ungrouped" value="Y"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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111 <param name="protected" value="Y"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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112 <output name="output" ftype="tabular">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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113 <assert_contents>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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114 <has_text text="GO:0000049|g__Bacteroides.s__Bacteroides_vulgatus" />
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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115 <has_text text="GO:0003866|g__Bacteroides.s__Bacteroides_vulgatus" />
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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116 </assert_contents>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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117 </output>
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118 </test>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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119 </tests>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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120 <help><![CDATA[
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121 @HELP_HEADER@
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122
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123 This tool takes a table of feature values and a mapping of groups to component features to produce
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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124 a new table with group values in place of feature values.
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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125
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126 HUMAnN gene family output can contain a very large number of features depending on the complexity
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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127 of your underlying sample. One way to explore this information in a simplified manner is via HUMAnN's
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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128 own pathway coverage and abundance, which summarize the values of their member genes. However, this
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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129 approach does not apply to gene families that are not associated with metabolic pathways.
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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130
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131 To further simplify the exploration of gene family abundance data, users can regroup gene families
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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132 into other functional categories using the current tool. This tool takes as arguments a gene
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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133 family abundance table and a mapping (groups) file that indicates which gene families belong to which
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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134 groups.
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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135
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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136 Out of the box, HUMAnN can regroup gene families to MetaCyc reactions (a step which is also
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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137 used internally as part of MetaCyc pathway quantification). Users can use additional mapping files
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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138 for both UniRef90 and UniRef50 gene families to the following systems:
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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139
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140 - MetaCyc Reactions
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141 - KEGG Orthogroups (KOs)
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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142 - Pfam domains
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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143 - Level-4 enzyme commission (EC) categories
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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144 - EggNOG (including COGs)
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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145 - Gene Ontology (GO)
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146 - Informative GO
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147
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148 In most cases, mappings are directly inferred from the annotation of the corresponding UniRef centroid sequence in UniProt.
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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149
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150 One exception to this are the "informative GO" (infogo1000) maps: These are informative subsets of GO computed from UniProt's
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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151 annotations and the structure of the GO hierarchy specifically for HUMAnN (each informative GO term has >1,000 UniRef centroids
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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152 annotated to it, but none of its progeny terms have >1,000 centroids so annotated).
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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153
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154 If the "UNMAPPED" gene abundance feature is included in a user's input, it will automatically be carried forward to the final output.
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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155 In addition, genes that do not group with a non-trivial feature are combined as an "UNGROUPED" group. By default, UNGROUPED reflects
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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156 the total abundance of genes that did not belong to another group (similar in spirit to the "UNINTEGRATED" value reported in the pathway
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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157 abundance file).
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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158
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159
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160 Some groups are not associated by default with human-readable names. To attach names to a regrouped table, use the HUMAnN rename tool
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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161 (The "GO" name map can be used for both raw GO and informative GO.)
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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162
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163 Inputs
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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164 ======
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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165
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166 Users are free to create and use additional mapping files and pass them to this tool. The format of a mapping file is:
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167
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168 ``
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169 group1 uniref1 uniref2 uniref3 ...
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170 ``
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171
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172 ``
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173 group2 uniref1 uniref5 ...
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174 ``
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175
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176 Where spaces between items above denote TABS. By default, feature abundances (such as gene families) are summed to produce group abundances.
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177
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178
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179
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180 ]]></help>
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181 <expand macro="citations"/>
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182 </tool>