# HG changeset patch
# User devteam
# Date 1377541222 14400
# Node ID a7a49d31c5cf318caf9bb442d66825288e076002

Uploaded tool tarball.

diff -r 000000000000 -r a7a49d31c5cf sam_merge.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_merge.xml	Mon Aug 26 14:20:22 2013 -0400
@@ -0,0 +1,62 @@
+<tool id="sam_merge2" name="Merge BAM Files" version="1.1.2">
+  <description>merges BAM files together</description>
+  <requirements>
+    <requirement type="package" version="1.56.0">picard</requirement>
+  </requirements>
+  <command>
+java -Xmx2G -jar \$JAVA_JAR_PATH/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__
+      #for $i in $inputs
+        I=${i.input}
+      #end for 
+    2&gt; $outlog
+    || echo "Error running Picard MergeSamFiles" >&amp;2
+  </command>
+  <inputs>
+    <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
+       help="This name will appear in your history so use it to remember what the new file in your history contains" />
+    <param name="mergeSD" value="true" type="boolean"  label="Merge all component bam file headers into the merged bam file"
+      truevalue="true" falsevalue="false" checked="yes" 
+      help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
+    <param name="input1" label="First file" type="data" format="bam,sam" />
+    <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
+    <repeat name="inputs" title="Input Files">
+      <param name="input" label="Add file" type="data" format="bam,sam" />
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="bam" name="output1" label="${title}.bam" />
+    <data format="txt" name="outlog" label="${title}_${tool.name}.log" />
+  </outputs>
+  <tests>
+    <!-- TODO: add ability to test framework to test without at least 
+         one repeat element value
+    -->
+    <test>
+      <param name="title" value="test1" />
+      <param name="mergeSD" value="true" />
+      <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> 
+      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
+      <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
+      <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/>
+    </test>
+    <test>
+      <param name="title" value="test2" />
+      <param name="mergeSD" value="true" />
+      <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> 
+      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
+      <param name="input" value="sam_merge_in3.bam" ftype="bam" />
+      <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
+      <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
+metadata such as read groups
+
+.. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
+
+  </help>
+</tool>
diff -r 000000000000 -r a7a49d31c5cf test-data/sam_merge_in1.bam
Binary file test-data/sam_merge_in1.bam has changed
diff -r 000000000000 -r a7a49d31c5cf test-data/sam_merge_in2.bam
Binary file test-data/sam_merge_in2.bam has changed
diff -r 000000000000 -r a7a49d31c5cf test-data/sam_merge_in3.bam
Binary file test-data/sam_merge_in3.bam has changed
diff -r 000000000000 -r a7a49d31c5cf test-data/sam_merge_out1.bam
Binary file test-data/sam_merge_out1.bam has changed
diff -r 000000000000 -r a7a49d31c5cf test-data/sam_merge_out1.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_merge_out1.log	Mon Aug 26 14:20:22 2013 -0400
@@ -0,0 +1,5 @@
+[Thu Aug 04 13:48:49 EST 2011] net.sf.picard.sam.MergeSamFiles INPUT=[/data/tmp/tmpjnE9mC/database/files/000/dataset_1.dat, /data/tmp/tmpjnE9mC/database/files/000/dataset_2.dat, /data/tmp/tmpjnE9mC/database/files/000/dataset_2.dat] OUTPUT=/data/tmp/tmpjnE9mC/database/files/000/dataset_3.dat MERGE_SEQUENCE_DICTIONARIES=true VALIDATION_STRINGENCY=LENIENT    SORT_ORDER=coordinate ASSUME_SORTED=false USE_THREADING=false TMP_DIR=/tmp/rlazarus VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+INFO	2011-08-04 13:48:49	MergeSamFiles	Sorting input files using temp directory /tmp/rlazarus
+INFO	2011-08-04 13:48:49	MergeSamFiles	Finished reading inputs.
+[Thu Aug 04 13:48:49 EST 2011] net.sf.picard.sam.MergeSamFiles done.
+Runtime.totalMemory()=2028732416
diff -r 000000000000 -r a7a49d31c5cf test-data/sam_merge_out2.bam
Binary file test-data/sam_merge_out2.bam has changed
diff -r 000000000000 -r a7a49d31c5cf test-data/sam_merge_out2.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_merge_out2.log	Mon Aug 26 14:20:22 2013 -0400
@@ -0,0 +1,5 @@
+[Thu Aug 04 13:49:53 EST 2011] net.sf.picard.sam.MergeSamFiles INPUT=[/data/tmp/tmpjnE9mC/database/files/000/dataset_5.dat, /data/tmp/tmpjnE9mC/database/files/000/dataset_6.dat, /data/tmp/tmpjnE9mC/database/files/000/dataset_7.dat] OUTPUT=/data/tmp/tmpjnE9mC/database/files/000/dataset_8.dat MERGE_SEQUENCE_DICTIONARIES=true VALIDATION_STRINGENCY=LENIENT    SORT_ORDER=coordinate ASSUME_SORTED=false USE_THREADING=false TMP_DIR=/tmp/rlazarus VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+INFO	2011-08-04 13:49:54	MergeSamFiles	Sorting input files using temp directory /tmp/rlazarus
+INFO	2011-08-04 13:49:54	MergeSamFiles	Finished reading inputs.
+[Thu Aug 04 13:49:54 EST 2011] net.sf.picard.sam.MergeSamFiles done.
+Runtime.totalMemory()=2028732416
diff -r 000000000000 -r a7a49d31c5cf tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 26 14:20:22 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="picard" version="1.56.0">
+        <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>