Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/venn.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
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children | fcc0778f6987 |
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<tool id="mothur_venn" name="Venn" version="1.15.0" force_history_refresh="True"> <description>Generate Venn diagrams gor groups </description> <command interpreter="python"> mothur_wrapper.py --cmd='venn' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.(\S+\.svg)$:svg' --READ_cmd='read.otu' #if $input.source == 'similarity': --READ_list=$input.otu #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: --READ_group='$otu_group' #end if #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --label='$input.label' #end if #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: --calc='$input.calc' #end if #elif $input.source == 'shared': --READ_shared=$input.otu #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --label='$input.label' #end if #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc='$calc' #end if $nseqs $permute #end if #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: --groups=$input.groups #end if </command> <inputs> <!-- get.relabund relabund type should also work --> <conditional name="input"> <param name="source" type="select" label="Generate Heatmap for"> <option value="similarity">OTU list</option> <option value="shared">OTU Shared</option> </param> <when value="similarity"> <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> <option value="sob">Chao</option> <option value="chao">Chao</option> <option value="ace">Ace</option> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> <options from_dataset="otu_group"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> </when> <when value="shared"> <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> <option value="sharedsobs">Shared Chao</option> <option value="sharedchao">Shared Chao</option> <option value="sharedace">Shared Ace</option> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> <options from_dataset="otu"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> </when> </conditional> <param name="nseqs" type="boolean" truevalue="--nseqs=true" falsevalue="" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/> <param name="permute" type="boolean" truevalue="--permute=true" falsevalue="" checked="false" label="permute - Create pictures with all possible 4-way permutations of groups"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> <requirement type="binary">mothur</requirement> </requirements> <tests> </tests> <help> **Mothur Overview** Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, provides bioinformatics for the microbial ecology community. .. _Mothur: http://www.mothur.org/wiki/Main_Page **Command Documenation** The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. .. _venn: http://www.mothur.org/wiki/Venn </help> </tool>