changeset 6:d9f3d4779507 draft default tip

v0.0.7 stricter error checking; record gnuplot version

--- a/tools/mummer/README.rst	Wed Feb 01 06:58:01 2017 -0500
+++ b/tools/mummer/README.rst	Wed May 10 12:14:49 2017 -0400
@@ -67,6 +67,10 @@
         - 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.
+v0.0.7  - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
+        - Wrapper script catches missing output explicitly.
+        - Capture gnuplot version as well.
 ======= ======================================================================
 
 
@@ -81,17 +85,17 @@
 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 -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
+    $ planemo shed_update -t testtoolshed --check_diff tools/mummer/
     ...
 
 or::
 
-    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
+    $ planemo shed_update -t toolshed --check_diff tools/mummer/
     ...
 
 To just build and check the tar ball, use::
 
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/mummer/
+    $ planemo shed_upload --tar_only tools/mummer/
     ...
     $ tar -tzf shed_upload.tar.gz 
     test-data/magic.pdf

--- a/tools/mummer/mummer.py	Wed Feb 01 06:58:01 2017 -0500
+++ b/tools/mummer/mummer.py	Wed May 10 12:14:49 2017 -0400
@@ -10,9 +10,9 @@
 """
 
 import os
+import shutil
 import sys
 import tempfile
-import shutil
 
 
 def run(cmd):
@@ -21,12 +21,15 @@
     if return_code:
         sys.exit("Error %i from: %s" % (return_code, cmd))
 
+
 if "-v" in sys.argv[1:]or "--version" in sys.argv[1:]:
-    print("MUMmer wrapper v0.0.3\n")
+    print("MUMmer wrapper v0.0.7\n")
     # TODO - How to get a version string from the mummer binary?
     os.system("nucmer --version")
     os.system("promer --version")
     os.system("mummerplot --version")
+    os.system("gnuplot --version")
+    # TODO - Should we include "gs --version" as a proxy for ps2pdf?
     sys.exit(0)
 
 # Parse Command Line
@@ -58,11 +61,17 @@
     cmd = '%s "%s" "%s"' % (algorithm, fasta_a, fasta_b)
 run(cmd)
 
+output_failed = False
+
 # PNG
 # ===
 cmd = 'mummerplot -R "%s" -Q "%s" --png --large --prefix=%s %s' % (fasta_a, fasta_b, prefix, coords)
 run(cmd)
-shutil.move(png_image, png_out)
+if os.path.isfile(png_image):
+    shutil.move(png_image, png_out)
+else:
+    sys.stderr.write("ERROR: PNG file not created.\n")
+    output_failed = True
 
 # PS --> PDF
 # ==========
@@ -74,9 +83,19 @@
 # Using "set size 1,1" works better - which is what --small gives:
 cmd = 'mummerplot -R "%s" -Q "%s" --postscript --small --prefix=%s %s' % (fasta_a, fasta_b, prefix, coords)
 run(cmd)
-cmd = 'ps2pdf -dEPSCrop "%s" "%s"' % (ps_image, pdf_out)
-run(cmd)
+if not os.path.isfile(ps_image):
+    sys.stderr.write("ERROR: PostScript file needed for PDF output was not created.\n")
+    output_failed = True
+else:
+    cmd = 'ps2pdf -dEPSCrop "%s" "%s"' % (ps_image, pdf_out)
+    run(cmd)
+    if not os.path.isfile(pdf_out):
+        sys.stderr.write("ERROR: PDF file not created.\n")
+        output_failed = True
 
 # Remove temp files...
 os.remove(coords)  # Might not be under the temp directory...
 shutil.rmtree(base_path)
+
+if output_failed:
+    sys.exit("ERROR: Failed to produce output file(s).")

--- a/tools/mummer/mummer.xml	Wed Feb 01 06:58:01 2017 -0500
+++ b/tools/mummer/mummer.xml	Wed May 10 12:14:49 2017 -0400
@@ -1,29 +1,18 @@
-<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.6">
+<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.7">
     <description>Combine mummer/nucmer/promer with mummerplot</description>
     <requirements>
             <!-- Needs ps2pdf from ghostscript -->      
-            <requirement type="binary">ps2pdf</requirement>
             <requirement type="package" version="9.10">ghostscript</requirement>
             <!-- Needs mummer, nucmer, promer and mummerplot from MUMmer -->
-            <requirement type="binary">mummer</requirement>
-            <requirement type="binary">nucmer</requirement>
-            <requirement type="binary">promer</requirement>
-            <requirement type="binary">mummerplot</requirement>
             <requirement type="package" version="3.23">mummer</requirement>
 	    <!-- mummerplot needs the gnuplot binary -->
-            <requirement type="binary">gnuplot</requirement>
             <requirement type="package" version="4.6">gnuplot</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">
-mummer.py --version
+    <version_command>
+python $__tool_directory__/mummer.py --version
     </version_command>
-    <command interpreter="python">
-mummer.py "$fasta_a" "$fasta_b" $algorithm "$png_output" "$pdf_output"
+    <command detect_errors="aggressive">
+python $__tool_directory__/mummer.py '$fasta_a' '$fasta_b' $algorithm '$png_output' '$pdf_output'
     </command>
     <inputs>
         <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->