Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/summary.tax.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 04 Dec 2012 11:05:19 -0600 |
parents | a6189f58fedb |
children | 95d75b35e4d2 |
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<tool id="mothur_summary_tax" name="Summary.tax" version="1.22.0"> <description>Assign sequences to taxonomy</description> <command interpreter="python"> mothur_wrapper.py --cmd='summary.tax' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tax\.summary$:'$tax_summary --outputdir='$logfile.extra_files_path' --taxonomy=$tax.taxonomy #if $name.__str__ != "None" and len($name.__str__) > 0: --name='$name' #end if #if $group.__str__ != "None" and len($group.__str__) > 0: --group='$group' #end if #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: --reftaxonomy=$reftax.taxonomy #end if </command> <inputs> <conditional name="tax"> <param name="source" type="select" label="Select Taxonomy from" help=""> <option value="hist">History</option> <option value="ref">Cached Reference</option> </param> <when value="ref"> <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"> <options from_file="mothur_taxonomy.loc"> <column name="name" index="0" /> <column name="value" index="1" /> </options> </param> </when> <when value="hist"> <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/> </when> </conditional> <param name="name" type="data" format="names" optional="true" label="name - taxonomy sequence names"/> <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/> <conditional name="reftax"> <param name="source" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static."> <option value="none">Selection is Optional</option> <option value="hist">History</option> <option value="ref">Cached Reference</option> </param> <when value="none"/> <when value="ref"> <param name="taxonomy" type="select" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"> <options from_file="mothur_taxonomy.loc"> <column name="name" index="0" /> <column name="value" index="1" /> </options> </param> </when> <when value="hist"> <param name="taxonomy" type="data" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/> </when> </conditional> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="summary" name="tax_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> <requirement type="package" version="1.27">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 summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information. .. _summary.tax: http://www.mothur.org/wiki/Summary.otu </help> </tool>