diff mothur/tools/mothur/dist.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/dist.seqs.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,72 @@
+<tool id="mothur_dist_seqs" name="Dist.seqs" version="1.15.0">
+ <description>calculate uncorrected pairwise distances between aligned sequences</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='dist.seqs'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.dist$:'$out_dist
+  --outputdir='$logfile.extra_files_path'
+  --fasta=$fasta
+  #if len($calc.__str__) > 0:
+   --calc=$calc
+  #end if
+  $countends
+  #if float($cutoff.__str__) > 0.0:
+   --cutoff=$cutoff
+  #end if
+  #if len($output.__str__) > 0:
+   --output=$output
+  #end if
+ </command>
+ <inputs>
+  <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/>
+  <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help="">
+   <option value="">use default</option>
+   <option value="onegap">onegap - counts a string of gaps as a single gap</option>
+   <option value="nogaps">nogaps - ignores gaps</option>
+   <option value="eachgap ">eachgap - penalize each gap</option>
+  </param>
+  <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="--countends=false" label="countends - Penalize terminal gaps"/>
+  <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
+                 help="Do not save any distances larger than this, a common value would be 0.10"/>
+  <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
+   <option value="">Default Column-Formatted Matrix</option>
+   <option value="lt">Phylip formatted Lower Triangle Matrix</option>
+   <option value="square">Phylip formatted Square Matrix</option>
+  </param>
+  <!--
+   oldfasta
+   column
+  -->
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="pair.dist" name="out_dist" label="${tool.name} on ${on_string}: dist">
+   <change_format>
+    <when input="output" value="lt" format="lower.dist" />
+    <when input="output" value="square" format="square.dist" />
+   </change_format>
+  </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 dist.seqs_ command will calculate uncorrected pairwise distances between aligned sequences.
+
+.. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs
+
+
+ </help>
+</tool>