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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author | iuc |
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date | Mon, 23 Apr 2018 09:35:06 -0400 |
parents | 8bfc093999ff |
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<tool profile="16.07" id="mothur_venn" name="Venn" version="@WRAPPER_VERSION@.0"> <description>Generate Venn diagrams for groups </description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$input.otu' input_otu.dat && echo 'venn( #if $input.source == "shared": shared=input_otu.dat, nseqs=$nseqs, permute=$permute, #if $input.groups: groups=${ str($input.groups).replace(",","-") }, #end if #elif $input.source == "similarity": list=input_otu.dat, abund=$input.abund, #end if #if $input.label: label=${ str($input.label).replace(",","-") }, #end if #if $input.calc: calc=${ str($input.calc).replace(",","-") }, #end if fontsize=$fontsize, sharedotus=$sharedotus )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <conditional name="input"> <param name="source" type="select" label="Generate Heatmap for"> <option value="shared">OTU Shared</option> <option value="similarity">OTU list</option> </param> <when value="shared"> <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> <option value="sharedsobs">Shared Sobs</option> <option value="sharedchao">Shared Chao</option> <option value="sharedace">Shared Ace</option> </param> <param name="label" type="select" multiple="true" label="label - OTU Labels"> <expand macro="labeloptions"/> </param> <param name="groups" type="select" multiple="true" label="groups - Groups to consider"> <options> <filter type="data_meta" ref="otu" key="groups"/> </options> </param> </when> <when value="similarity"> <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> <option value="sobs">Sobs</option> <option value="chao">Chao</option> <option value="ace">Ace</option> </param> <param name="abund" type="integer" value="10" min="5" label="abund - Abundance when using the ace calculator ( >= 5 )"/> <param name="label" type="select" multiple="true" label="label - OTU Labels"> <expand macro="labeloptions"/> </param> </when> </conditional> <param name="nseqs" type="boolean" falsevalue="false" truevalue="true" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/> <param name="permute" type="select" label="permute - Create pictures with all possible 4-way permutations of groups"> <option value="1">1</option> <option value="2">2</option> <option value="3">3</option> <option value="4" selected="true">4</option> <option value="true">true</option> </param> <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> <param name="sharedotus" type="boolean" falsevalue="false" truevalue="true" checked="true" label="sharedotus - This parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=T"/> <expand macro="param-savelog"/> </inputs> <outputs> <collection name="sharedotus_out" type="list" label="${tool.name} on ${on_string}: sharedotus"> <filter>sharedotus</filter> <discover_datasets pattern=".*?\.(?P<designation>.*)\.sharedotus" format="tabular"/> </collection> <collection name="svgs_out" type="list" label="${tool.name} on ${on_string}: svg"> <discover_datasets pattern=".*?\.(?P<designation>.*)\.svg" format="svg"/> </collection> <expand macro="logfile-output"/> </outputs> <tests> <test><!-- test with shared file --> <param name="source" value="shared"/> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <param name="calc" value="sharedsobs,sharedchao"/> <param name="groups" value="forest,pasture"/> <output_collection name="sharedotus_out" count="35"> <element name="0.05.sharedsobs.forest-pasture" md5="7513c9df64477a08b69f0d4665011e80" ftype="tabular" /> </output_collection> <output_collection name="svgs_out" count="72"> <element name="0.05.sharedsobs.forest-pasture" md5="e2dc0d5485520f5b22aa185ba91b123e" ftype="svg" /> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with list file --> <param name="source" value="similarity"/> <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <param name="calc" value="sobs,chao,ace"/> <param name="groups" value="forest,pasture"/> <output_collection name="svgs_out" count="108"> <element name=".0.45.ace" md5="d69778f507939bc2f5d2bbc3a0088f21" ftype="svg"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators .. _venn: https://www.mothur.org/wiki/Venn ]]></help> <expand macro="citations"/> </tool>