changeset 14:ee59e5cff3ba

Mothur - make.fastq fix command name and change_format on output fastq according to qual input, fastq.info outputs qual454
author Jim Johnson <jj@umn.edu>
date Wed, 05 Oct 2011 10:37:11 -0500
parents 4f797d3eee3a
children a6189f58fedb
files mothur/tools/mothur/make.fastq.xml
diffstat 1 files changed, 9 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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>