--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_fastq/bam_to_fastq-readme.txt	Tue Jun 07 16:27:36 2011 -0400
@@ -0,0 +1,9 @@
+Use Picard's SamToFastq program to convert BAM files to fastq. This makes it
+easy to store reads in Galaxy as compressed, accessible BAM files but then
+allow them to be extracted to feed into programs requiring fastq.
+
+Requires:
+  Picard (http://picard.sourceforge.net/)
+    The SamToFastq.jar file needs to be linked from this directory or available
+    in a standard directory like /usr/share/java/picard.
+  pysam (http://code.google.com/p/pysam/)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_fastq/bam_to_fastq.xml	Tue Jun 07 16:27:36 2011 -0400
@@ -0,0 +1,27 @@
+<tool id="bam_to_fastq" name="BAM to fastq" force_history_refresh="True" version="0.0.1">
+  <description>Convert BAM file to fastq</description>
+  <command interpreter="python">bam_to_fastq_wrapper.py $in_bam $out $out.id $__new_file_path__</command>
+  <inputs>
+    <param format="bam" name="in_bam" type="data" label="BAM file"/>
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="out" metadata_source="in_bam"/>
+  </outputs>
+
+<help>
+**What it does**
+
+Extract sequences and quality scores from a BAM file, converting into fastq files.
+
+**Input**
+
+A BAM alignment file. 
+
+**Output**
+
+Fastq files with sequence and quality data. Output qualities are in Sanger format.
+For single end data, one fastq file is produced; paired end data will have separate
+fastq files for the forward and reverse reads.
+</help>
+
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_fastq/bam_to_fastq_wrapper.py	Tue Jun 07 16:27:36 2011 -0400
@@ -0,0 +1,48 @@
+"""Wrapper script providing conversion from BAM to fastq, handling paired ends.
+
+Requires:
+  Picard (http://picard.sourceforge.net/)
+    The SamToFastq.jar file needs to be linked from this directory or available
+    in a standard directory like /usr/share/java/picard.
+  pysam (http://code.google.com/p/pysam/)
+"""
+import os
+import sys
+import subprocess
+
+import pysam
+
+def main(in_bam, out_fastq, out_id, extra_file_dir):
+    out_fastq2 = check_for_paired(in_bam, out_id, extra_file_dir)
+    picard_jar = find_picard_jar("SamToFastq")
+    opts = [("INPUT", in_bam), ("FASTQ", out_fastq),
+            ("QUIET", "true"), ("VERBOSITY", "WARNING")]
+    if out_fastq2:
+        opts.append(("SECOND_END_FASTQ", out_fastq2))
+    opts = ["%s=%s" % (x, y) for x, y in opts]
+    cl = ["java", "-jar", picard_jar] + opts
+    subprocess.check_call(cl)
+
+def find_picard_jar(name):
+    test_dirs = [os.path.dirname(__file__), "/usr/share/java/picard"]
+    for d in test_dirs:
+        f = os.path.join(d, "%s.jar" % name)
+        if os.path.exists(f):
+            return f
+    raise ValueError("Could not find %s in %s" % (name, test_dirs))
+
+def check_for_paired(in_bam, out_id, extra_file_dir):
+    if is_paired(in_bam):
+        return os.path.join(extra_file_dir, "%s_%s_%s_%s_%s" %
+                            ('primary', out_id, 'pair2', 'visible', 'fastqsanger'))
+    else:
+        return None
+
+def is_paired(in_bam):
+    samfile = pysam.Samfile(in_bam, "rb")
+    read = samfile.fetch(until_eof=True).next()
+    samfile.close()
+    return read.is_paired
+
+if __name__ == "__main__":
+    main(*sys.argv[1:])