# HG changeset patch
# User peterjc
# Date 1384344315 18000
# Node ID 93b8db68dde451034717d7cbdfb9fe1b39595cab
# Parent  6564815949e0b601576ba08d82faf233e64842e9
Uploaded v0.0.1b, fixed dependency

diff -r 6564815949e0 -r 93b8db68dde4 tools/samtools_idxstats/README.rst
--- a/tools/samtools_idxstats/README.rst	Mon Nov 11 12:31:47 2013 -0500
+++ b/tools/samtools_idxstats/README.rst	Wed Nov 13 07:05:15 2013 -0500
@@ -62,7 +62,7 @@
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder::
 
-    $ tar -czf samtools_idxstats.tar.gz tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/repository_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular
+    $ tar -czf samtools_idxstats.tar.gz tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/tool_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular
 
 Check this worked::
 
@@ -70,7 +70,7 @@
     tools/samtools_idxstats/README.rst
     tools/samtools_idxstats/samtools_idxstats.xml
     tools/samtools_idxstats/samtools_idxstats.py
-    tools/samtools_idxstats/repository_dependencies.xml
+    tools/samtools_idxstats/tool_dependencies.xml
     test-data/ex1.bam
     test-data/ex1.idxstats.tabular
 
diff -r 6564815949e0 -r 93b8db68dde4 tools/samtools_idxstats/repository_dependencies.xml
--- a/tools/samtools_idxstats/repository_dependencies.xml	Mon Nov 11 12:31:47 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="This requires the samtools 0.1.19 binaries">
-    <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-</repositories>
diff -r 6564815949e0 -r 93b8db68dde4 tools/samtools_idxstats/samtools_idxstats.py
--- a/tools/samtools_idxstats/samtools_idxstats.py	Mon Nov 11 12:31:47 2013 -0500
+++ b/tools/samtools_idxstats/samtools_idxstats.py	Wed Nov 13 07:05:15 2013 -0500
@@ -32,9 +32,11 @@
 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)
+    stop_err("Input BAM file not found: %s" % bam_filename)
 if not os.path.isfile(bai_filename):
-   stop_err("Input BAI file not found: %s" % 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()
diff -r 6564815949e0 -r 93b8db68dde4 tools/samtools_idxstats/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/samtools_idxstats/tool_dependencies.xml	Wed Nov 13 07:05:15 2013 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>