Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/sens.spec.xml @ 12:370b3fc4e7d3
Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 09 Aug 2011 11:39:27 -0500 |
parents | e990ac8a0f58 |
children | bfbaf823be4c |
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<tool id="mothur_sens_spec" name="Sens.spec" version="1.19.0" > <description>Determine the quality of OTU assignment</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path --cmd='sens.spec' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sensspec$:'$sensspec --outputdir='$logfile.extra_files_path' --list=$list #if isinstance($dist.datatype, $__app__.datatypes_registry.get_datatype_by_extension('pair.dist').__class__): --column=$dist #else --phylip=$dist #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if len($precision.__str__) > 0: --precision=$precision #end if #if float($cutoff.__str__) > 0.0: --cutoff=$cutoff #end if $hard </command> <inputs> <param name="list" type="data" format="list" label="list - OTU List"/> <param name="dist" type="data" format="dist" label="phylip,column - Distance Matrix"/> <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> <options from_dataset="list"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="precision" type="integer" value="100" optional="true" label="precision - Precision for rounding distance values"/> <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/> <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="sensspec" label="${tool.name} on ${on_string}: sensspec" /> </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 sens.spec_ command takes a list_ and either a column_ or phylip_ distance matrix to determine the quality of OTU assignment. .. _list: http://www.mothur.org/wiki/List_file .. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix .. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _sens.spec: http://www.mothur.org/wiki/Sens.spec </help> </tool>