# HG changeset patch
# User peterjc
# Date 1431527652 14400
# Node ID 242f1a5a9277a745f5edeabc34895f1375635f8e
# Parent  3070949d8fd7850037d0838742274bcb30c9cf0e
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats commit ddda833946bc691eacf9c116695bda3a1bbdbf19

diff -r 3070949d8fd7 -r 242f1a5a9277 tools/samtools_idxstats/README.rst
--- a/tools/samtools_idxstats/README.rst	Fri Nov 21 07:02:43 2014 -0500
+++ b/tools/samtools_idxstats/README.rst	Wed May 13 10:34:12 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for samtools idxstats
 ====================================
 
-This wrapper is copyright 2013-2014 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.
 
@@ -52,6 +52,8 @@
 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).
 ======= ======================================================================
 
 
@@ -61,20 +63,30 @@
 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)
diff -r 3070949d8fd7 -r 242f1a5a9277 tools/samtools_idxstats/samtools_idxstats.py
--- a/tools/samtools_idxstats/samtools_idxstats.py	Fri Nov 21 07:02:43 2014 -0500
+++ b/tools/samtools_idxstats/samtools_idxstats.py	Wed May 13 10:34:12 2015 -0400
@@ -21,22 +21,22 @@
     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()
@@ -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))
diff -r 3070949d8fd7 -r 242f1a5a9277 tools/samtools_idxstats/samtools_idxstats.xml
--- a/tools/samtools_idxstats/samtools_idxstats.xml	Fri Nov 21 07:02:43 2014 -0500
+++ b/tools/samtools_idxstats/samtools_idxstats.xml	Wed May 13 10:34:12 2015 -0400
@@ -1,9 +1,14 @@
-<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.3">
+<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" />
diff -r 3070949d8fd7 -r 242f1a5a9277 tools/samtools_idxstats/tool_dependencies.xml
--- a/tools/samtools_idxstats/tool_dependencies.xml	Fri Nov 21 07:02:43 2014 -0500
+++ b/tools/samtools_idxstats/tool_dependencies.xml	Wed May 13 10:34:12 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>