Mercurial > repos > jjohnson > mothur_toolsuite
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/bootstrap.shared.xml Tue Jun 07 17:35:35 2011 -0400 @@ -0,0 +1,126 @@ +<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>