Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/chimera.perseus.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | ec8df51e841a |
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<tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.24.0" > <description>Find putative chimeras using chimeraCheck</description> <command interpreter="python"> mothur_wrapper.py --cmd='chimera.perseus' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file,'^\S+\.perseus\.accnos$:'$out_accnos --outputdir='$logfile.extra_files_path' --fasta=$fasta #if isinstance($name.datatype, $__app__.datatypes_registry.get_datatype_by_extension('name').__class__): --name=$name #else --count=$name #end if #if $group.__str__ != "None" and len($group.__str__) > 0: --group='$group' #end if #if $alpha.__str__ != '': --alpha=$alpha #end if #if $beta.__str__ != '': --beta=$beta #end if #if $cutoff.__str__ != '': --cutoff=$cutoff #end if --processors=8 $dereplicate </command> <inputs> <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> <param name="name" type="data" format="names,count" label="name - Names or count_table"/> <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/> <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/> <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> <param name="dereplicate" type="boolean" falsevalue="" truevalue="--dereplicate=true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" /> <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: perseus.accnos" /> </outputs> <requirements> <requirement type="package" version="1.33">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 chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences. .. _chimera.perseus: http://www.mothur.org/wiki/Chimera.perseus </help> </tool>