Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/chop.seqs.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
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<tool id="mothur_chop_seqs" name="Chop.seqs" version="1.20.0"> <description>Trim sequences to a specified length</description> <command interpreter="python"> mothur_wrapper.py --cmd='chop.seqs' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+.chop\.fasta$:'$out_fasta --outputdir='$logfile.extra_files_path' --fasta=$fasta --numbases=$numbases --keep=$keep $countgaps $short --processors=8 #if $name.__str__ != "None": --name=$name #end if #if $group.__str__ != "None": --group=$group #end if #if $count.__str__ != "None": --count=$count #end if </command> <inputs> <param name="fasta" type="data" format="fasta,align" label="fasta - Sequences to be chopped"/> <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/> <param name="keep" type="select" label="keep - Part of the sequence to keep"> <option value="front">front</option> <option value="back">back</option> </param> <param name="countgaps" type="boolean" truevalue="--countgaps=true" falsevalue="" checked="false" label="countgaps - Count gaps as bases"/> <param name="short" type="boolean" truevalue="--short=true" falsevalue="" checked="false" label="short - keep sequences that are too short to chop"/> <param name="name" type="data" format="name" label="name file" optional="true"/> <param name="group" type="data" format="group" label="group file" optional="true"/> <param name="count" type="data" format="count_table" label="count file" optional = "true"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" /> </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 chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences. .. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0 </help> </tool>