Mercurial > repos > iuc > humann2_regroup_table
diff humann2_regroup_table.xml @ 0:a1747df2bc21 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
| author | iuc |
|---|---|
| date | Mon, 13 Mar 2017 12:38:02 -0400 |
| parents | |
| children | 1d141730ec69 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/humann2_regroup_table.xml Mon Mar 13 12:38:02 2017 -0400 @@ -0,0 +1,115 @@ +<tool id="humann2_regroup_table" name="Regroup" version="@WRAPPER_VERSION@.0"> + <description> a HUMAnN2 generated table by features</description> + <macros> + <import>humann2_macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version"/> + <command detect_errors="exit_code"><![CDATA[ + humann2_regroup_table + --input '$input' + -o '$output_table' + --function '$function' + + #if $built_in.built_in_test == "true": + --groups '$built_in.gene_family_groups.groups' + #else: + --custom '$built_in.custom' + $built_in.reversed + #end if + + --ungrouped '$ungrouped' + --protected '$protected' + ]]></command> + <inputs> + <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> + <param argument="--function" type="select" label="How to combine grouped features?"> + <option value="sum" selected="true">Sum</option> + <option value="mean">Mean</option> + </param> + <conditional name="built_in"> + <param name="built_in_test" type="select" label="Use built-in grouping options?" help=""> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <conditional name="gene_family_groups"> + <param name="gene_family_type" type="select" label="Gene family type"> + <option value="uniref50">UniRef50 gene families</option> + <option value="uniref90">UniRef90 gene families</option> + </param> + <when value="uniref50"> + <param name="groups" type="select" label="Grouping options" help="(--groups)"> + <option value="uniref50_go">UniRef50 gene families into GO</option> + <option value="uniref50_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option> + <option value="uniref50_eggnog">UniRef50 gene families into eggNOG</option> + <option value="uniref50_pfam">UniRef50 gene families into PFAM</option> + <option value="uniref50_level4ec">UniRef50 gene families into level4ec</option> + <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option> + <option value="uniref50_rxn">UniRef50 gene families into metacyc reactions</option> + </param> + </when> + <when value="uniref90"> + <param name="groups" type="select" label="Grouping options" help="(--groups)"> + <option value="uniref90_go">UniRef90 gene families into GO</option> + <option value="uniref90_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option> + <option value="uniref90_eggnog">UniRef90 gene families into eggNOG</option> + <option value="uniref90_pfam">UniRef90 gene families into PFAM</option> + <option value="uniref90_level4ec">UniRef90 gene families into level4ec</option> + <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option> + <option value="uniref90_rxn">UniRef90 gene families into metacyc reactions</option> + </param> + </when> + </conditional> + </when> + <when value="false"> + <param argument="--custom" type="data" format="tsv" label="Custom groups file"/> + <param argument="--reversed" type="boolean" checked="false" truevalue="--reversed" falsevalue="" label="Is the groups file reversed?" help="Mapping from features to groups"/> + </when> + </conditional> + <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/> + <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?"/> + <param argument="--protected" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Carry through protected features, such as 'UNMAPPED'?"/> + </inputs> + <outputs> + <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" /> + </outputs> + <tests> + <test> + <param name="input" value="demo_genefamilies.tsv"/> + <param name="function" value="sum"/> + <param name="built_in_test" value="true"/> + <param name="gene_family_type" value="uniref90"/> + <param name="groups" value="uniref90_infogo1000"/> + <param name="ungrouped" value="Y"/> + <param name="protected" value="Y"/> + <output name="output_table" file="regrouped_gene_families_to_infogo1000.tsv"/> + </test> + <test> + <param name="input" value="demo_genefamilies.tsv"/> + <param name="function" value="mean"/> + <param name="built_in_test" value="true"/> + <param name="gene_family_type" value="uniref90"/> + <param name="groups" value="uniref90_ko"/> + <param name="ungrouped" value="Y"/> + <param name="protected" value="Y"/> + <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/> + </test> + <test> + <param name="input" value="demo_genefamilies.tsv"/> + <param name="function" value="sum"/> + <param name="built_in_test" value="true"/> + <param name="gene_family_type" value="uniref90"/> + <param name="groups" value="uniref90_rxn"/> + <param name="ungrouped" value="Y"/> + <param name="protected" value="Y"/> + <output name="output_table" file="regrouped_gene_families_to_rxn.tsv"/> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +Regroup HUMAnN2 table features is a tool for regrouping table features (abundances or coverage) given a table of feature values and a mapping of groups to component features. It produces a new table with group values in place of feature values. + ]]></help> + <expand macro="citations"/> +</tool>