Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/dist.shared.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 |
parents | |
children | fcc0778f6987 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/dist.shared.xml Tue Jun 07 17:32:23 2011 -0400 @@ -0,0 +1,121 @@ +<tool id="mothur_dist_shared" name="Dist.shared" version="1.15.0" force_history_refresh="True"> + <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='dist.shared' + --result='^mothur.\S+\.logfile$:'$logfile + --outputdir='$logfile.extra_files_path' + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + #if len($output.__str__) > 0: + #if $output.__str__ == 'square': + --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:square.dist' + #elif $output.__str__ == 'lt': + --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:lower.dist' + #end if + #else: + --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:lower.dist' + #end if + --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 $calc.__str__ != "None" and len($calc.__str__) > 0: + --calc=$calc + #end if + #if $output.__str__ != "None" and len($output.__str__) > 0: + --output=$output + #end if + </command> + <inputs> + <!-- list,group or shared --> + <conditional name="input"> + <param name="source" type="select" label="Generate Collector Curvers 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"/> + <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_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_calulators.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="output" type="select" label="output - Distance Matrix Output Format" help=""> + <option value="lt">Phylip formatted Lower Triangle Matrix</option> + <option value="square">Phylip formatted Square Matrix</option> + </param> + </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 dist.shared_ command will generate a phylip-formatted distance matrix that describes the dissimilarity (1-similarity) among multiple groups. + +.. _dist.shared: http://www.mothur.org/wiki/Dist.shared + + + </help> +</tool>