Mercurial > repos > iuc > humann2_rename_table
diff humann2_rename_table.xml @ 1:b6d4c448782f draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author | iuc |
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date | Tue, 01 Aug 2017 07:55:21 -0400 |
parents | dd4b5b9daf6b |
children | 252ae00df89c |
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--- a/humann2_rename_table.xml Mon Mar 13 12:37:08 2017 -0400 +++ b/humann2_rename_table.xml Tue Aug 01 07:55:21 2017 -0400 @@ -6,47 +6,74 @@ <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ - humann2_rename_table - --input '$input' - -o '$output_table' - --names '$names' - $simplify - #if $custom - --custom '$custom' - #end if +humann2_rename_table + --input '$input' + -o '$output_table' + #if $renaming.type == 'standard' + --names '$renaming.names' + #else + --custom '$renaming.custom' + #end if + $simplify ]]></command> <inputs> <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> - <param argument="--names" type="select" label="Table features that can be renamed"> - <option value="metacyc-rxn" selected="true">MetaCyc reactions</option> - <option value="metacyc-pwy">MetaCyc pathways</option> - <option value="infogo1000">InfoGO1000</option> - <option value="uniref90">UniRef90</option> - <option value="kegg-module">KEGG Module</option> - <option value="ec">Enzyme commision (EC)</option> - <option value="go">Gene Ontology (GO)</option> - <option value="pfam">PFAM</option> - <option value="eggnog">eggNOG</option> - <option value="uniref50">UniRef50</option> - <option value="kegg-pathway">KEGG Pathway</option> - <option value="kegg-orthology">KEGG Orthology</option> - </param> - <param argument="--simplify" type="boolean" checked="false" truevalue="--simplify" falsevalue="" label="Remove non-alphanumeric characters from names?"/> - <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"/> + <conditional name="renaming"> + <param name="type" type="select" label="Type of renaming"> + <option value="standard">Standard renaming</option> + <option value="custom">Custom renaming</option> + </param> + <when value="standard"> + <param argument="--names" type="select" label="Table features that can be renamed"> + <option value="metacyc-rxn" selected="true">MetaCyc reactions</option> + <option value="metacyc-pwy">MetaCyc pathways</option> + <option value="infogo1000">InfoGO1000</option> + <option value="kegg-module">KEGG Module</option> + <option value="ec">Enzyme commision (EC)</option> + <option value="go">Gene Ontology (GO)</option> + <option value="pfam">PFAM</option> + <option value="eggnog">eggNOG</option> + <option value="uniref50">UniRef50</option> + <!--<option value="uniref90">UniRef90</option>--> + <option value="kegg-pathway">KEGG Pathway</option> + <option value="kegg-orthology">KEGG Orthology</option> + </param> + </when> + <when value="custom"> + <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"/> + </when> + </conditional> + <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" checked="false" label="Remove non-alphanumeric characters from names?"/> </inputs> <outputs> <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" /> </outputs> <tests> <test> - <param name="input" value="demo_genefamilies.tsv"/> - <param name="names" value="uniref90" /> + <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/> + <conditional name="renaming"> + <param name="type" value="standard"/> + <param name="names" value="infogo1000" /> + </conditional> <param name="simplify" value=""/> <output name="output_table"> <assert_contents> - <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" /> - <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" /> - <has_text text="UniRef90_C3RF26: HRDC domain protein" /> + <has_text text="GO:0000015: [CC] phosphopyruvate hydratase complex" /> + <has_text text="GO:0000287: [MF] magnesium ion binding" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/> + <conditional name="renaming"> + <param name="type" value="custom"/> + <param name="custom" value="rename_mapping" /> + </conditional> + <param name="simplify" value=""/> + <output name="output_table"> + <assert_contents> + <has_text text="GO:0000015: GO1" /> + <has_text text="GO:0000107: NO_NAME" /> </assert_contents> </output> </test>