Mercurial > repos > bebatut > humann2_rename_table

annotate humann2_rename_table.xml @ 5:ffba4cba95c7 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f45f31529390153bdaf93a3c94a65f6888ed484b\n'-dirty
author bebatut
date Fri, 03 Mar 2017 06:27:03 -0500
parents 993b75cba608
children
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1 <tool id="humann2_rename_table" name="Rename" version="@WRAPPER_VERSION@.0">
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2 <description>features of a HUMAnN2 generated table</description>
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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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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_rename_table --version
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14 ]]>
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15 </version_command>
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17 <command><![CDATA[
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18 humann2_rename_table
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19 --input '$input'
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20 -o '$output_table'
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21 --names '$names'
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22 $simplify
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23 #if $custom
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24 --custom '$custom'
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25 #end if
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26 ]]></command>
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27
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28 <inputs>
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29 <param argument="--input" type="data" format="tsv" label="Gene/pathway table"/>
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30
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31 <param argument="--names" type="select" label="Table features that can be renamed">
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32 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
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33 <option value="metacyc-pwy">MetaCyc pathways</option>
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34 <option value="infogo1000">InfoGO1000</option>
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35 <option value="uniref90">UniRef90</option>
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36 <option value="kegg-module">KEGG Module</option>
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37 <option value="ec">Enzyme commision (EC)</option>
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38 <option value="go">Gene Ontology (GO)</option>
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39 <option value="pfam">PFAM</option>
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40 <option value="eggnog">eggNOG</option>
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41 <option value="uniref50">UniRef50</option>
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42 <option value="kegg-pathway">KEGG Pathway</option>
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43 <option value="kegg-orthology">KEGG Orthology</option>
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44 </param>
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45 <param argument='--simplify' type='boolean' checked="false" truevalue='--simplify' falsevalue='' label="Remove non-alphanumeric characters from names?"/>
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46 <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" optional="true"/>
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47 </inputs>
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48
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49 <outputs>
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50 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
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51 </outputs>
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52
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53 <tests>
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54 <test>
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55 <param name="input" value="demo_genefamilies.tsv"/>
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56 <param name="names" value="uniref90" />
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57 <param name='simplify' value=""/>
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58 <output name="output_table">
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59 <assert_contents>
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60 <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" />
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61 <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" />
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62 <has_text text="UniRef90_C3RF26: HRDC domain protein" />
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67
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68 <help><![CDATA[
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69 **What it does**
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70
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71 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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72
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73 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
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74 ]]></help>
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75
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76 <expand macro="citations"/>
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77 </tool>