From b8fd7dbe2e9cd367c0db2026e910d044cd3322bd Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 19 May 2011 10:07:53 -0400
Subject: [PATCH] Add Picard and fastqc tools to Main

---
 tool_conf.xml.main | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 8cd708b1a97..a3d3214fc20 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -351,6 +351,8 @@
         <tool file="fastx_toolkit/fastx_renamer.xml" />
         <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
         <tool file="fastx_toolkit/fastx_trimmer.xml" />
+    <label text="FASTQ QC" id="fastq_qc" />
+        <tool file="rgenetics/rgFastQC.xml" />
   </section>
   <section name="NGS: Mapping" id="ngs_mapping">
     <label text="Illumina" id="illumina"/>
@@ -394,6 +396,21 @@
    <label text="Filtering" id="filtering" />
       <tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
   </section>
+  <section name="NGS: Picard (beta)" id="picard_beta">
+    <label text="QC/Metrics for sam/bam" id="qcsambam"/>
+    <tool file="picard/picard_BamIndexStats.xml" />
+    <tool file="picard/rgPicardASMetrics.xml" />
+    <tool file="picard/rgPicardGCBiasMetrics.xml" />
+    <tool file="picard/rgPicardLibComplexity.xml" />
+    <tool file="picard/rgPicardInsertSize.xml" />
+    <tool file="picard/rgPicardHsMetrics.xml" />
+  <label text="bam/sam Cleaning" id="picard-clean" />
+    <tool file="picard/picard_AddOrReplaceReadGroups.xml" />
+    <tool file="picard/picard_ReorderSam.xml" />
+    <tool file="picard/picard_ReplaceSamHeader.xml" />
+    <tool file="picard/rgPicardFixMate.xml" />
+    <tool file="picard/rgPicardMarkDups.xml" />
+  </section>
   <label text="RGENETICS" id="rgenetics" />
   <section name="SNP/WGA: Data; Filters" id="rgdat">
   <label text="Data: Import and upload" id="rgimport" />