Mercurial > repos > peterjc > mummer

--- a/tools/mummer/README.rst	Wed Aug 05 11:34:31 2015 -0400
+++ b/tools/mummer/README.rst	Wed Feb 01 06:58:01 2017 -0500
@@ -1,7 +1,7 @@
 Galaxy wrapper for drawing dotplots using MUMmer 3
 ==================================================

-This wrapper is copyright 2014-2015 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2014-2016 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.

@@ -65,6 +65,8 @@
         - Test case added.
 v0.0.5  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.6  - PEP8 style changes to Python script (internal change only).
+        - Fixed display of input parameter help text.
 ======= ======================================================================


@@ -79,12 +81,12 @@
 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/mummer/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
     ...

 or::

-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
     ...

 To just build and check the tar ball, use::
--- a/tools/mummer/mummer.py	Wed Aug 05 11:34:31 2015 -0400
+++ b/tools/mummer/mummer.py	Wed Feb 01 06:58:01 2017 -0500
@@ -14,17 +14,14 @@
 import tempfile
 import shutil

-def sys_exit( msg ):
-    sys.stderr.write("%s\n" % msg)
-    sys.exit(1)

 def run(cmd):
     print(cmd)
     return_code = os.system(cmd)
     if return_code:
-        sys_exit("Error %i from: %s" % (return_code, cmd))
+        sys.exit("Error %i from: %s" % (return_code, cmd))

-if "-v" in sys.argv [1:]or "--version" in sys.argv[1:]:
+if "-v" in sys.argv[1:]or "--version" in sys.argv[1:]:
     print("MUMmer wrapper v0.0.3\n")
     # TODO - How to get a version string from the mummer binary?
     os.system("nucmer --version")
@@ -32,29 +29,29 @@
     os.system("mummerplot --version")
     sys.exit(0)

-#Parse Command Line
-#TODO - optparse
+# Parse Command Line
+# TODO - optparse
 try:
     fasta_a, fasta_b, algorithm, png_out, pdf_out = sys.argv[1:]
-except:
-    sys_exit("Expect 5 arguments, got %i" % (len(sys.argv) - 1))
+except ValueError:
+    sys.exit("Expect 5 arguments, got %i" % (len(sys.argv) - 1))


 valid_algo = ["mummer", "nucmer", "promer"]
 if algorithm not in valid_algo:
-    sys_exit("Invalid algorithm argument %r, should be: %s" % (algorithm, ", ".join(valid_algo)))
+    sys.exit("Invalid algorithm argument %r, should be: %s" % (algorithm, ", ".join(valid_algo)))

 base_path = tempfile.mkdtemp()
 prefix = os.path.join(base_path, "ref_qry")
 coords = prefix + ".mums"
-#gnuplot = prefix + ".gp"
+# gnuplot = prefix + ".gp"
 ps_image = prefix + ".ps"
 png_image = prefix + ".png"

 if algorithm == "mummer":
-    #Add -mum as per example to find maximal unique matches between ref and query.
-    #Add the -b -c options to search both strands and report relative to forward strand
-    #which then matches the default dual-strand approach in nucmer and promer
+    # Add -mum as per example to find maximal unique matches between ref and query.
+    # Add the -b -c options to search both strands and report relative to forward strand
+    # which then matches the default dual-strand approach in nucmer and promer
     cmd = '%s -mum -b -c "%s" "%s" > %s' % (algorithm, fasta_a, fasta_b, coords)
 else:
     coords = "out.delta"
@@ -80,6 +77,6 @@
 cmd = 'ps2pdf -dEPSCrop "%s" "%s"' % (ps_image, pdf_out)
 run(cmd)

-#Remove temp files...
-os.remove(coords) # Might not be under the temp directory...
+# Remove temp files...
+os.remove(coords)  # Might not be under the temp directory...
 shutil.rmtree(base_path)
--- a/tools/mummer/mummer.xml	Wed Aug 05 11:34:31 2015 -0400
+++ b/tools/mummer/mummer.xml	Wed Feb 01 06:58:01 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.5">
+<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.6">
     <description>Combine mummer/nucmer/promer with mummerplot</description>
     <requirements>
             <!-- Needs ps2pdf from ghostscript -->
@@ -29,10 +29,10 @@
         <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->
         <param name="fasta_a" type="data" format="fasta"
 	       label="Species A"
-	       description="Nucleotide FASTA file, e.g. contigs from genome assembly." />
+	       help="Nucleotide FASTA file, e.g. contigs from genome assembly." />
         <param name="fasta_b" type="data" format="fasta"
 	       label="Species B"
-	       description="Nucleotide FASTA file, e.g. contigs from genome assembly." />
+	       help="Nucleotide FASTA file, e.g. contigs from genome assembly." />
         <param name="algorithm" type="select" label="MUMmer search algorithm">
             <option value="mummer">mummer, efficiently locates maximal unique matches between two sequences</option>
             <option value="nucmer">NUCmer (NUCleotide MUMmer), for closely related sequences</option>
--- a/tools/mummer/tool_dependencies.xml	Wed Aug 05 11:34:31 2015 -0400
+++ b/tools/mummer/tool_dependencies.xml	Wed Feb 01 06:58:01 2017 -0500
@@ -7,6 +7,6 @@
         <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="gnuplot" version="4.6">
-        <repository changeset_revision="1b3a60daf8fb" name="package_gnuplot_4_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="2d356c5a1354" name="package_gnuplot_4_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>