# HG changeset patch
# User fangly
# Date 1317704532 14400
# Node ID 27a15723d4f0c21ca9a8bdb7b26729ef87f43876
# Parent  7d26d64539b2197baf260a9b1f89b9d8b15db567
Uploaded

diff -r 7d26d64539b2 -r 27a15723d4f0 Galaxy_readme.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy_readme.txt	Tue Oct 04 01:02:12 2011 -0400
@@ -0,0 +1,5 @@
+An XML wrapper that provides a GUI for Grinder in Galaxy (http://galaxy.psu.edu/)
+
+Place these files in your Galaxy directory. More information at http://wiki.g2.bx.psu.edu/FrontPage.
+
+Note: The Grinder wrapper uses Galaxy buitin datasets located in the 'all_fasta' data table.
diff -r 7d26d64539b2 -r 27a15723d4f0 tools/ngs_simulation/grinder.xml
--- a/tools/ngs_simulation/grinder.xml	Mon Sep 19 01:07:28 2011 -0400
+++ b/tools/ngs_simulation/grinder.xml	Tue Oct 04 01:02:12 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="grinder" name="Grinder" version="0.3.7" force_history_refresh="True">
+<tool id="grinder" name="Grinder" version="0.3.8" force_history_refresh="True">
 
   <!--
     Author: florent.angly@gmail.com
@@ -9,7 +9,7 @@
     • Better sync with Grinder parameters, defaults and help
   -->
 
-  <description>genomic, metagenomic and amplicon read simulator (BETA)</description>
+  <description>genomic, metagenomic and amplicon read simulator</description>
 
   <requirements>
     <requirement type="binary">grinder</requirement>
@@ -101,6 +101,9 @@
       #if str($qual_levels):
         -qual_levels      $qual_levels
       #end if
+      #if str($fastq_output):
+        -fastq_output     $fastq_output
+      #end if
       #if str($profile_file) != "None":
         -profile_file     $profile_file.value
       #end if
@@ -215,6 +218,10 @@
 
     <param name="qual_levels" type="text" optional="true" label="Quality score levels" help="Generate basic quality scores for the simulated reads. Good residues are given a specified good score (e.g. 30) and residues that are the result of an insertion or substitution are given a specified bad score (e.g. 10). Specify first the good score and then the bad score, e.g. '30 10'" />
 
+    <param name="fastq_output" type="boolean" truevalue="1" falsevalue="0" checked="false" label="FASTQ output" help="
+Write the generated reads in FASTQ format (Sanger variant) instead of FASTA and
+QUAL. Quality score levels need to be specified for this option to be effective." />
+
     <param name="profile_file" type="data" format="txt" optional="true" label="Profile file" help="A file that contains Grinder arguments. This is useful if you use many options or often use the same options. Lines with comments (#) are ignored. Consider the profile file, 'simple_profile.txt':
 
     # A simple Grinder profile
diff -r 7d26d64539b2 -r 27a15723d4f0 tools/ngs_simulation/grinder_multiple_outputs.py
--- a/tools/ngs_simulation/grinder_multiple_outputs.py	Mon Sep 19 01:07:28 2011 -0400
+++ b/tools/ngs_simulation/grinder_multiple_outputs.py	Tue Oct 04 01:02:12 2011 -0400
@@ -50,6 +50,10 @@
         # Assign the dataset format
         if extension == '.txt': 
            format = 'text'
+        elif extension == '.fq':
+           format = 'fastqsanger'
+        elif extension == '.fastq':
+           format = 'fastqsanger'
         elif extension == '.fa':
            format = 'fasta'
         elif extension == '.fna':
@@ -58,10 +62,6 @@
            format = 'fasta'
         elif extension == '.fasta':
            format = 'fasta'
-        elif extension == '.fq':
-           format = 'fastq'
-        elif extension == '.fastq':
-           format = 'fastq'
         elif extension == '.qual':
            format = 'qual'
         else:
@@ -72,7 +72,7 @@
         match = q.search(basename)
         if match != None:
           lib_num = match.group(1)
-          name = 'lib%s' % lib_num
+          name = 'lib%s-' % lib_num
 
         match = r.search(basename)
         if match == None:
@@ -82,11 +82,12 @@
         if format == 'qual':
           lib_type = 'qual'
 
-        name = name + '-' + lib_type        
+        name = name + lib_type        
 
         # Move the dataset to the proper place
-        optional_spec = 'asdf'
-        destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s_%s' % ( output_id, name, format, optional_spec ) )
+        #db_ref = ''
+        #destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s_%s' % (output_id, name, format, db_ref) )
+        destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s' % (output_id, name, format) )
 
         print "moving %s to %s" % (source, destination)