Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/summary.single.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 |
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children | fcc0778f6987 |
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<tool id="mothur_summary_single" name="Summary.single" version="1.15.0" force_history_refresh="True"> <description>Summary of calculator values for OTUs</description> <command interpreter="python"> mothur_wrapper.py --cmd='summary.single' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+\.((\S+?)\.summary)$:tabular' --READ_cmd='read.otu' --READ_list=$otu #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: --READ_group='$otu_group' #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc='$calc' #end if #if int($abund.__str__) > 0: --abund=$abund #end if #if int($size.__str__) > 0: --size=$size #end if $groupmode </command> <inputs> <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> <param name="otu_group" type="data" format="groups" optional="true" label="read.otu(group=) - Group file for the OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> <options from_file="mothur_calulators.loc"> <column name="mult" index="1"/> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="static_value" name="mult" column="1" value="single" /> </options> </param> <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/> <param name="size" type="integer" value="0" label="size - "/> <param name="groupmode" type="boolean" truevalue="--groupmode=true" falsevalue="--groupmode=false" checked="true" label="groupmode - Collate shared summary results in one file"/> </inputs> <outputs> <data format="html" name="logfile" label="${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 summary.single_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group file. .. _summary.single: http://www.mothur.org/wiki/Summary.single </help> </tool>