Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/summary.seqs.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 | 49058b1f8d3f |
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<tool id="mothur_summary_seqs" name="Summary.seqs" version="1.20.0"> <description>Summarize the quality of sequences</description> <command interpreter="python"> mothur_wrapper.py --cmd='summary.seqs' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$out_summary --outputdir='$logfile.extra_files_path' --fasta=$fasta #if $name.__str__ != "None" and len($name.__str__) > 0: --name=$name #end if #if $count.__str__ != "None" and len($count.__str__) > 0: --count=$count #end if --processors=8 </command> <inputs> <param name="fasta" type="data" format="fasta,align" label="fasta - Dataset"/> <param name="name" type="data" format="names" label="name - Names" optional="true"/> <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" /> </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 summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. .. _summary.seqs: http://www.mothur.org/wiki/Summary.seqs </help> </tool>