From 54b4dd64b5754b05256b7cf082b8ea8d3a298045 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 08:52:13 -0500
Subject: [PATCH] Add picard_FastqToSam.xml and picard_SamToFastq.xml to
 tool_conf.xml.main.

---
 tool_conf.xml.main                 | 3 +++
 tools/picard/picard_FastqToSam.xml | 3 ++-
 tools/picard/picard_SamToFastq.xml | 3 ++-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 34f94f96206..2d4ec0dfec6 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -406,6 +406,9 @@
       <tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
   </section>
   <section name="NGS: Picard (beta)" id="picard_beta">
+    <label text="Conversion" id="picard_conversion"/>
+    <tool file="picard/picard_FastqToSam.xml" />
+    <tool file="picard/picard_SamToFastq.xml" />
     <label text="QC/Metrics for sam/bam" id="qcsambam"/>
     <tool file="picard/picard_BamIndexStats.xml" />
     <tool file="picard/rgPicardASMetrics.xml" />
diff --git a/tools/picard/picard_FastqToSam.xml b/tools/picard/picard_FastqToSam.xml
index 2f736b3be96..9dec7c65edc 100644
--- a/tools/picard/picard_FastqToSam.xml
+++ b/tools/picard/picard_FastqToSam.xml
@@ -1,6 +1,7 @@
 <tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">
   <description>creates an unaligned BAM file</description>
-  <requirements><requirement type="package">picard</requirement></requirements>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <!-- Dan Blankenberg -->
   <command>java  -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar"
     FASTQ="${input_fastq1}"
diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml
index 278f42934c6..e0e71a9b7c7 100644
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -1,6 +1,7 @@
 <tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.0">
   <description>creates a FASTQ file</description>
-  <requirements><requirement type="package">picard</requirement></requirements>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <!-- Dan Blankenberg -->
   <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar"
     INPUT="${input_sam}"