Mercurial > repos > iuc > humann2_rename_table

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
author iuc
date Mon, 13 Mar 2017 12:37:08 -0400
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children b6d4c448782f
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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[
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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 --names '$names'
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13 $simplify
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14 #if $custom
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15 --custom '$custom'
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
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20 <param argument="--names" type="select" label="Table features that can be renamed">
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21 <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
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22 <option value="metacyc-pwy">MetaCyc pathways</option>
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23 <option value="infogo1000">InfoGO1000</option>
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24 <option value="uniref90">UniRef90</option>
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25 <option value="kegg-module">KEGG Module</option>
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26 <option value="ec">Enzyme commision (EC)</option>
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27 <option value="go">Gene Ontology (GO)</option>
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28 <option value="pfam">PFAM</option>
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29 <option value="eggnog">eggNOG</option>
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30 <option value="uniref50">UniRef50</option>
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31 <option value="kegg-pathway">KEGG Pathway</option>
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32 <option value="kegg-orthology">KEGG Orthology</option>
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33 </param>
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34 <param argument="--simplify" type="boolean" checked="false" truevalue="--simplify" falsevalue="" label="Remove non-alphanumeric characters from names?"/>
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35 <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"/>
dd4b5b9daf6b planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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36 </inputs>
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37 <outputs>
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38 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input" value="demo_genefamilies.tsv"/>
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43 <param name="names" value="uniref90" />
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44 <param name="simplify" value=""/>
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45 <output name="output_table">
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46 <assert_contents>
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47 <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" />
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48 <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" />
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49 <has_text text="UniRef90_C3RF26: HRDC domain protein" />
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 @HELP_HEADER@
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56
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57 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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58 ]]></help>
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59 <expand macro="citations"/>
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60 </tool>