Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/split.abund.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_split_abund" name="Split.abund" version="1.15.0" force_history_refresh="True"> <description>Separate sequences into rare and abundant groups</description> <command interpreter="python"> mothur_wrapper.py --cmd='split.abund' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.abund\.list$:'$abund_list,'^\S+\.rare\.list$:'$rare_list,'^\S+\.rare\.accnos$:'$rare_accnos,'^\S+\.abund\.accnos$:'$abund_accnos --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.fasta)$:fasta','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.groups)$:groups','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.accnos)$:accnos' --fasta=$fasta #if $search.type == "list": --list=$search.input #if $search.label.__str__ != "None" and len($search.label.__str__) > 0: --label=$search.label #end if #elif $search.type == "name": --name=$search.input #end if --cutoff=$cutoff #if $group.__str__ != "None" and len($group.__str__) > 0: --group=$group #end if #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if $accnos </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> <conditional name="search"> <param name="type" type="select" label="Type to screen" help=""> <option value="list">OTU List</option> <option value="name">Name reference</option> </param> <when value="name"> <param name="input" type="data" format="names" label="name - Name reference"/> </when> <when value="list"> <param name="input" type="data" format="list" label="list - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="input"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> </when> </conditional> <param name="cutoff" type="integer" value="10" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/> <param name="group" type="data" format="groups" optional="true" label="group - Group dataset"/> <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true"> <options from_dataset="group"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> <param name="accnos" type="boolean" truevalue="--accnos=true" falsevalue="" checked="false" label="accnos - Produce rare and abundant Accession outputs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="list" name="abund_list" label="${tool.name} on ${on_string}: abund.list" /> <data format="list" name="rare_list" label="${tool.name} on ${on_string}: rare.list" /> <data format="accnos" name="rare_accnos" label="${tool.name} on ${on_string}: rare.accnos"> <filter>accnos == True</filter> </data> <data format="accnos" name="abund_accnos" label="${tool.name} on ${on_string}: abund.accnos"> <filter>accnos == True</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 split.abund_ command reads a fasta file and a list or a names file and splits the sequences into rare and abundant groups. .. _split.abund: http://www.mothur.org/wiki/Split.abund </help> </tool>