changeset 6:2f6466b40dbf draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats commit 4bd49529e9ca2096cd875e98daf7190d13fa8d0b-dirty

--- a/tools/samtools_idxstats/README.rst	Thu May 21 10:58:28 2015 -0400
+++ b/tools/samtools_idxstats/README.rst	Wed Feb 01 13:15:58 2017 -0500
@@ -68,12 +68,12 @@
 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_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
     ...
 
 or::
 
-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
     ...
 
 To just build and check the tar ball, use::

--- a/tools/samtools_idxstats/samtools_idxstats.py	Thu May 21 10:58:28 2015 -0400
+++ b/tools/samtools_idxstats/samtools_idxstats.py	Wed Feb 01 13:15:58 2017 -0500
@@ -12,33 +12,27 @@
 """
 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
+    # Galaxy seems to invert the order of the two lines
     print "(Galaxy wrapper v0.0.2)"
     cmd = "samtools 2>&1 | grep -i ^Version"
     sys.exit(os.system(cmd))
 
-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:
-   sys_exit("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):
-    sys_exit("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":
-        sys_exit("Error: Galaxy did not index your BAM file")
-    sys_exit("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:
+# 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")
@@ -48,14 +42,14 @@
 assert os.path.isfile(bai_file), bai_file
 assert os.path.isfile(bam_file + ".bai"), bam_file
 
-#Run samtools idxstats:
+# Run samtools idxstats:
 cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename)
 return_code = os.system(cmd)
 
-#Remove the temp symlinks:
+# Remove the temp symlinks:
 os.remove(bam_file)
 os.remove(bai_file)
 os.rmdir(tmp_dir)
 
 if return_code:
-    sys_exit("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/tool_dependencies.xml	Thu May 21 10:58:28 2015 -0400
+++ b/tools/samtools_idxstats/tool_dependencies.xml	Wed Feb 01 13:15:58 2017 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>