Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/bootstrap.shared.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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<tool id="mothur_bootstrap_shared" name="Bootstrap.shared" version="1.16.0" force_history_refresh="True"> <description>Generate a newick trees for dissimilarity among groups</description> <command interpreter="python"> #* 98_sq_phylip_amazon.fn.jclass.bootunique.tre 98_sq_phylip_amazon.fn.thetayc.bootunique.tre 98_sq_phylip_amazon.fn.jclass.bootunique.cons.pairs 98_sq_phylip_amazon.fn.jclass.bootunique.cons.tre 98_sq_phylip_amazon.fn.thetayc.bootunique.cons.pairs 98_sq_phylip_amazon.fn.thetayc.bootunique.cons.tre 98_sq_phylip_amazon.fn.jclass.boot0.00.tre 98_sq_phylip_amazon.fn.thetayc.boot0.00.tre 98_sq_phylip_amazon.fn.jclass.boot0.00.cons.pairs 98_sq_phylip_amazon.fn.jclass.boot0.00.cons.tre 98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.pairs 98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.tre *# mothur_wrapper.py --cmd='bootstrap.shared' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.pairs)$:txt' --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: --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 #end if #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: --groups=$input.groups #end if #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc=$calc #end if #if int($iters.__str__) > 0: --iters=$iters #end if </command> <inputs> <!-- list,group or shared --> <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="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="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> <options from_file="mothur_calculators.loc"> <column name="mult2" index="2"/> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="static_value" name="mult2" column="2" value="shar" /> </options> </param> <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/> </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 bootstrap.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. .. _bootstrap.shared: http://www.mothur.org/wiki/Bootstrap.shared </help> </tool>