# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1354285164 21600
# Node ID 561fa7324f6050f90fbc737c86e5c66061d1723a
# Parent  3cfe418109492c83f8abab32182bd792c4f9bdfa
Add make.contigs

diff -r 3cfe41810949 -r 561fa7324f60 mothur/tools/mothur/make.contigs.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/make.contigs.xml	Fri Nov 30 08:19:24 2012 -0600
@@ -0,0 +1,106 @@
+<tool id="mothur_make_contigs" name="Make.contigs" version="1.26.0">
+ <description>Aligns paired forard and reverse fastq files to contigs as fasta and quality</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='make.contigs'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.contigs\.fasta$:'$fasta,'^\S+\.contigs\.qual$:'$qual,'^\S+\.contigs\.mismatch$:'$mismatch
+  --outputdir='$logfile.extra_files_path'
+  --ffastq=$ffastq
+  --rfastq=$rfastq
+  --align=$align
+  #if $oligo.add == "yes":
+   --oligos=$oligo.oligos
+   #if $oligo.bdiffs.__str__ != '' and int($oligo.bdiffs.__str__) > 0:
+    --bdiffs=$oligo.bdiffs
+   #end if
+   #if $oligo.pdiffs.__str__ != '' and int($oligo.pdiffs.__str__) > 0:
+    --pdiffs=$oligo.pdiffs
+   #end if
+   #if $oligo.tdiffs.__str__ != '' and int($oligo.tdiffs.__str__) > 0:
+    --tdiffs=$oligo.tdiffs
+   #end if
+  #end if
+
+  #if $match.__str__ != '':
+   --match=$match
+  #end if
+  #if $mismatch.__str__ != '':
+   --mismatch=$mismatch
+  #end if
+  #if $gapopen.__str__ != '':
+   --gapopen=$gapopen
+  #end if
+  #if $gapextend.__str__ != '':
+   --gapextend=$gapextend
+  #end if
+  #if $threshold.__str__ != '':
+   --threshold=$threshold
+  #end if
+  --processors=8
+ </command>
+ <inputs>
+  <param name="ffastq" type="data" format="fastq" label="ffastq - Forward Fastq Sequence file"/>
+  <param name="rfastq" type="data" format="fastq" label="rfastq - Reverse Fastq Sequence file"/>
+  <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
+   <option value="gotoh" selected="true">gotoh (default)</option>
+   <option value="needleman">needleman</option>
+  </param>
+  <conditional name="oligo">
+   <param name="add" type="select" label="Trim with an oligos file?" help="">
+    <option value="no">no</option>
+    <option value="yes">yes</option>
+   </param>
+   <when value="no"/>
+   <when value="yes">
+    <param name="oligos" type="data" format="oligos" optional="true" label="oligos - barcodes and primers"
+           help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. 
+                Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, 
+                and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file.  "/>
+    <param name="bdiffs" type="integer" value="0" label="bdiffs - number of differences to allow in the barcode (default 0)">
+      <validator type="in_range" message="Number of differences can't be negative" min="0"/>
+    </param>
+    <param name="pdiffs" type="integer" value="0" label="pdiffs - number of differences to allow in the primer (default 0)">
+      <validator type="in_range" message="Number of differences can't be negative" min="0"/>
+    </param>
+    <param name="tdiffs" type="integer" value="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)">
+      <validator type="in_range" message="Number of differences can't be negative" min="0"/>
+    </param>
+   </when>
+  </conditional>
+  <param name="match" type="integer" value="1" optional="true" label="match - Pairwise alignment reward for a match"/>
+  <param name="mismatch" type="integer" value="-1" optional="true" label="mismatch - Pairwise alignment penalty for a mismatch"/>
+  <param name="gapopen" type="integer" value="-2" optional="true" label="gapopen - Pairwise alignment penalty for opening a gap"/>
+  <param name="gapextend" type="integer" value="-1" optional="true" label="gapextend - Pairwise alignment penalty for extending a gap"/>
+  <param name="threshold" type="integer" value="40" optional="true" label="threshold - for quality scores" 
+         help="When we are merging the overlapping regions, in the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it.">
+      <validator type="in_range" message="threshold can't be negative" min="0"/>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="fasta" name="fasta" label="${tool.name} on ${on_string}: contigs.fasta"/>
+  <data format="qual" name="qual" label="${tool.name} on ${on_string}: contigs.qual"/>
+  <data format="txt" name="mismatch" label="${tool.name} on ${on_string}: contigs.mismatch"/>
+ </outputs>
+ <requirements>
+  <requirement type="package" version="1.27">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 make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.
+
+.. _make.contigs: http://www.mothur.org/wiki/Make.contigs
+
+ </help>
+</tool>