Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/pca.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
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children | e990ac8a0f58 |
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<tool id="mothur_pca" name="Pca" version="1.16.0"> <description>generate principle components plot data</description> <command interpreter="python"> mothur_wrapper.py ## 98_sq_phylip_amazon.fn.unique.pca.axes ## 98_sq_phylip_amazon.fn.unique.pca.loadings --cmd='pca' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pca.axes$:'$pca_axes,'^\S+\.pca.loadings$:'$pca_loadings --outputdir='$logfile.extra_files_path' --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 $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: --READ_groups='$input.groups' #end if #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --READ_label='$input.label' #end if #elif $input.source == 'shared': --READ_shared=$input.otu #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --READ_label='$input.label' #end if #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: --READ_groups='$input.groups' #end if #end if $metric </command> <inputs> <conditional name="input"> <param name="source" type="select" label="Generate principle components for"> <option value="similarity">OTU list</option> <option value="shared">OTU Shared</option> </param> <when value="similarity"> <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> <options from_dataset="otu_group"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> </when> <when value="shared"> <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="unique_value" name="unq_lbl" column="0" /> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> <options from_dataset="otu"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> </when> </conditional> <param name="metric" type="boolean" truevalue="" falsevalue="--Metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" /> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="axes" name="pca_axes" label="${tool.name} on ${on_string}: pca.axes" /> <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" /> </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 pca_ command generate principle components plot data. .. _pca: http://www.mothur.org/wiki/Pca </help> </tool>