Mercurial > repos > iuc > humann2_rename_table

annotate humann2_rename_table.xml @ 1:b6d4c448782f draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author iuc
date Tue, 01 Aug 2017 07:55:21 -0400
parents dd4b5b9daf6b
children 252ae00df89c
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dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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1 <tool id="humann2_rename_table" name="Rename" version="@WRAPPER_VERSION@.0">
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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2 <description>features of a HUMAnN2 generated table</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[
1
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9 humann2_rename_table
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10 --input '$input'
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11 -o '$output_table'
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12 #if $renaming.type == 'standard'
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13 --names '$renaming.names'
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14 #else
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15 --custom '$renaming.custom'
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16 #end if
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17 $simplify
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18 ]]></command>
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19 <inputs>
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20 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
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21 <conditional name="renaming">
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22 <param name="type" type="select" label="Type of renaming">
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23 <option value="standard">Standard renaming</option>
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24 <option value="custom">Custom renaming</option>
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25 </param>
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26 <when value="standard">
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27 <param argument="--names" type="select" label="Table features that can be renamed">
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28 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
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29 <option value="metacyc-pwy">MetaCyc pathways</option>
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30 <option value="infogo1000">InfoGO1000</option>
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31 <option value="kegg-module">KEGG Module</option>
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32 <option value="ec">Enzyme commision (EC)</option>
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33 <option value="go">Gene Ontology (GO)</option>
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34 <option value="pfam">PFAM</option>
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35 <option value="eggnog">eggNOG</option>
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36 <option value="uniref50">UniRef50</option>
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37 <!--<option value="uniref90">UniRef90</option>-->
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38 <option value="kegg-pathway">KEGG Pathway</option>
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39 <option value="kegg-orthology">KEGG Orthology</option>
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40 </param>
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41 </when>
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42 <when value="custom">
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43 <param argument="--custom" type="data" format="tsv" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value"/>
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44 </when>
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45 </conditional>
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46 <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" checked="false" label="Remove non-alphanumeric characters from names?"/>
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47 </inputs>
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48 <outputs>
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49 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
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50 </outputs>
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51 <tests>
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52 <test>
1
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53 <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/>
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54 <conditional name="renaming">
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55 <param name="type" value="standard"/>
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56 <param name="names" value="infogo1000" />
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57 </conditional>
0
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58 <param name="simplify" value=""/>
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59 <output name="output_table">
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60 <assert_contents>
1
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61 <has_text text="GO:0000015: [CC] phosphopyruvate hydratase complex" />
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62 <has_text text="GO:0000287: [MF] magnesium ion binding" />
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63 </assert_contents>
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64 </output>
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65 </test>
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66 <test>
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67 <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/>
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68 <conditional name="renaming">
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69 <param name="type" value="custom"/>
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70 <param name="custom" value="rename_mapping" />
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71 </conditional>
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72 <param name="simplify" value=""/>
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73 <output name="output_table">
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74 <assert_contents>
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75 <has_text text="GO:0000015: GO1" />
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76 <has_text text="GO:0000107: NO_NAME" />
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77 </assert_contents>
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78 </output>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 @HELP_HEADER@
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83
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84 Rename HUMAnN2 table features is a tool for renaming table features given a custom mapping. The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new valu
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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85 ]]></help>
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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86 <expand macro="citations"/>
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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87 </tool>