Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/heatmap.sim.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 7bfe1f843858 |
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<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.19.0" force_history_refresh="True"> <description>Generate a heatmap for pariwise similarity</description> <command interpreter="python"> mothur_wrapper.py --cmd='heatmap.sim' --outputdir='$logfile.extra_files_path' #if $as_datasets.__str__ == "yes": #if $input.source == 'shared': --result='^mothur.\S+\.logfile$:'$logfile --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg' #else: --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.heatmap\.sim\.svg$:'$heatmap #end if #else: --result='^mothur.\S+\.logfile$:'$logfile #end if #if $input.source == 'shared': --shared=$input.otu #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --label='$input.label' #end if #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: --groups=$input.groups #end if #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: --calc='$input.calc' #end if #elif $input.source == 'column': --column=$input.dist --name=$input.name #elif $input.source == 'phylip': --phylip=$input.dist #end if </command> <inputs> <conditional name="input"> <param name="source" type="select" label="Generate Heatmap for"> <option value="shared">shared - Sample Similarity - OTU Shared</option> <option value="phylip">phylip - Phylip Distance Matrix</option> <option value="column">colomn - Pairwise Column Distance Matrix</option> </param> <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 include" 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> <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> </when> <when value="column"> <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> <param name="name" type="data" format="names" label="name - Names"/> </when> <when value="phylip"> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> </when> </conditional> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="svg" name="heatmap" label="${tool.name} on ${on_string}: heatmap.sim.svg"> <filter>as_datasets != 'true' and input['source'] != 'shared'</filter> </data> </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 heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators .. _shared: http://www.mothur.org/wiki/Shared_file .. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix .. _name: http://www.mothur.org/wiki/Name_file .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim </help> </tool>