--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/samtools_idxstats/samtools_idxstats.py	Wed Nov 20 12:27:33 2013 -0500
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+"""Wrapper for "samtools idxstats" for use in Galaxy.
+
+This script takes exactly three command line arguments:
+ * Input BAM filename
+ * Input BAI filename (via Galaxy metadata)
+ * Output tabular filename
+
+This messes about with the filenames to make samtools happy, then
+runs "samtools idxstats" and captures the output to the desired
+tabular file.
+"""
+import sys
+import os
+import subprocess
+import tempfile
+
+if "-v" in sys.argv or "--version" in sys.argv:
+    #Galaxy seems to invert the order of the two lines
+    print "(Galaxy wrapper v0.0.1)"
+    cmd = "samtools 2>&1 | grep -i ^Version"
+    sys.exit(os.system(cmd))
+
+def stop_err(msg, error_level=1):
+   """Print error message to stdout and quit with given error level."""
+   sys.stderr.write("%s\n" % msg)
+   sys.exit(error_level)
+
+if len(sys.argv) != 4:
+   stop_err("Require three arguments: BAM, BAI, tabular filenames")
+
+bam_filename, bai_filename, tabular_filename = sys.argv[1:]
+
+if not os.path.isfile(bam_filename):
+    stop_err("Input BAM file not found: %s" % bam_filename)
+if not os.path.isfile(bai_filename):
+    if bai_filename == "None":
+        stop_err("Error: Galaxy did not index your BAM file")
+    stop_err("Input BAI file not found: %s" % bai_filename)
+
+#Assign sensible names with real extensions, and setup symlinks:
+tmp_dir = tempfile.mkdtemp()
+bam_file = os.path.join(tmp_dir, "temp.bam")
+bai_file = os.path.join(tmp_dir, "temp.bam.bai")
+os.symlink(os.path.abspath(bam_filename), bam_file)
+os.symlink(os.path.abspath(bai_filename), bai_file)
+assert os.path.isfile(bam_file), bam_file
+assert os.path.isfile(bai_file), bai_file
+assert os.path.isfile(bam_file + ".bai"), bam_file
+
+#Run samtools idxstats:
+cmd = "samtools idxstats %s > %s" % (bam_file, tabular_filename)
+return_code = os.system(cmd)
+
+#Remove the temp symlinks:
+os.remove(bam_file)
+os.remove(bai_file)
+os.rmdir(tmp_dir)
+
+if return_code:
+    stop_err("Return code %i from command:\n%s" % (return_code, cmd))