# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1317829031 18000
# Node ID ee59e5cff3ba96de9b3025d1bfebaf542122e987
# Parent  4f797d3eee3abf3adb34be707ec8e1feea8ee44a
Mothur - make.fastq fix command name and change_format on output fastq according to qual input, fastq.info outputs qual454

diff -r 4f797d3eee3a -r ee59e5cff3ba mothur/tools/mothur/make.fastq.xml
--- a/mothur/tools/mothur/make.fastq.xml	Wed Oct 05 10:34:44 2011 -0500
+++ b/mothur/tools/mothur/make.fastq.xml	Wed Oct 05 10:37:11 2011 -0500
@@ -2,7 +2,7 @@
  <description>Convert fasta and quality to fastq</description>
  <command interpreter="python">
   mothur_wrapper.py 
-  --cmd='fastq.info'
+  --cmd='make.fastq'
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq
   --outputdir='$logfile.extra_files_path'
   --fasta=$fasta
@@ -14,7 +14,14 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq"/>
+  <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq">
+   <change_format>
+    <when input="qfile.ext" value="qual454" format="fastqsanger"/>
+    <when input="qfile.ext" value="qualillumina" format="fastqillumina"/>
+    <when input="qfile.ext" value="qualsolexa" format="fastqsolexa"/>
+    <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/>
+   </change_format>
+  </data>
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>