--- a/tools/samtools_idxstats/README.rst	Wed Nov 20 12:27:33 2013 -0500
+++ b/tools/samtools_idxstats/README.rst	Wed May 13 10:35:50 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for samtools idxstats
 ====================================
 
-This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -26,19 +26,19 @@
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a ``tools/samtools_idxstats`` folder:
 
-* samtools_idxstats.xml (the Galaxy tool definition)
-* samtools_idxstats.py (the Python wrapper script)
-* README.rst (this file)
+* ``samtools_idxstats.xml`` (the Galaxy tool definition)
+* ``samtools_idxstats.py`` (the Python wrapper script)
+* ``README.rst`` (this file)
 
 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
 the tool. Just add the line, perhaps under the NGS tools section::
 
   <tool file="samtools_idxstats/samtools_idxstats.xml" />
 
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id samtools_idxstats
+    $ ./run_tests.sh -id samtools_idxstats
 
 That's it.
 
@@ -50,29 +50,43 @@
 Version Changes
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial public release
+v0.0.2  - Use quoted filenames when calling samtools (in case of spaces etc)
+v0.0.3  - Embed samtools citation in tool XML.
+v0.0.4  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
 Developers
 ==========
 
-Development is one this GitHub repository:
+Development is on this GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
 
-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/tool_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
+    ...
 
-Check this worked::
+or::
+
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
+    ...
 
-    $ tar -tzf 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
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/samtools_idxstats/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
     test-data/ex1.bam
     test-data/ex1.idxstats.tabular
+    tools/samtools_idxstats/README.rst
+    tools/samtools_idxstats/samtools_idxstats.py
+    tools/samtools_idxstats/samtools_idxstats.xml
+    tools/samtools_idxstats/tool_dependencies.xml
 
 
 Licence (MIT)

--- a/tools/samtools_idxstats/samtools_idxstats.py	Wed Nov 20 12:27:33 2013 -0500
+++ b/tools/samtools_idxstats/samtools_idxstats.py	Wed May 13 10:35:50 2015 -0400
@@ -17,26 +17,26 @@
 
 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)"
+    print "(Galaxy wrapper v0.0.2)"
     cmd = "samtools 2>&1 | grep -i ^Version"
     sys.exit(os.system(cmd))
 
-def stop_err(msg, error_level=1):
+def sys_exit(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")
+   sys_exit("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)
+    sys_exit("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)
+        sys_exit("Error: Galaxy did not index your BAM file")
+    sys_exit("Input BAI file not found: %s" % bai_filename)
 
 #Assign sensible names with real extensions, and setup symlinks:
 tmp_dir = tempfile.mkdtemp()
@@ -49,7 +49,7 @@
 assert os.path.isfile(bam_file + ".bai"), bam_file
 
 #Run samtools idxstats:
-cmd = "samtools idxstats %s > %s" % (bam_file, tabular_filename)
+cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename)
 return_code = os.system(cmd)
 
 #Remove the temp symlinks:
@@ -58,4 +58,4 @@
 os.rmdir(tmp_dir)
 
 if return_code:
-    stop_err("Return code %i from command:\n%s" % (return_code, cmd))
+    sys_exit("Return code %i from command:\n%s" % (return_code, cmd))

--- a/tools/samtools_idxstats/samtools_idxstats.xml	Wed Nov 20 12:27:33 2013 -0500
+++ b/tools/samtools_idxstats/samtools_idxstats.xml	Wed May 13 10:35:50 2015 -0400
@@ -1,9 +1,14 @@
-<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.1">
+<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4">
     <description>samtools idxstats</description>
     <requirements>
         <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <version_command interpreter="python">samtools_idxstats.py --version</version_command>
     <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command>
     <inputs>
@@ -12,11 +17,6 @@
     <outputs>
         <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" />
     </outputs>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <tests>
         <test>
             <param name="input_bam" value="ex1.bam" ftype="bam" />
@@ -73,4 +73,7 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    </citations>
 </tool>

--- a/tools/samtools_idxstats/tool_dependencies.xml	Wed Nov 20 12:27:33 2013 -0500
+++ b/tools/samtools_idxstats/tool_dependencies.xml	Wed May 13 10:35:50 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>