diff mothur/tools/mothur/chop.seqs.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/chop.seqs.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,50 @@
+<tool id="mothur_chop_seqs" name="Chop.seqs" version="1.15.0">
+ <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
+  $short
+ </command>
+ <inputs>
+  <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
+  <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
+  <param name="keep" type="select" label="keep - Part of the sequence to keep">
+   <option value="front">front</option>
+   <option value="back">back</option>
+  </param>
+  <param name="countgaps" type="boolean" truevalue="--countgaps=true" falsevalue="" checked="false" label="countgaps - Count gaps as bases"/>
+  <param name="short" type="boolean" truevalue="--short=true" falsevalue="" checked="false" label="short - keep sequences that are too short to chop"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" />
+ </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 chop.seqs_ command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. It works on both aligned and unaligned sequences.
+
+.. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs
+
+
+ </help>
+</tool>