changeset 6:0f6eb4a75000 draft

v0.0.15 internal changes; v0.0.14 fixed error handling

--- a/tools/effectiveT3/README.rst	Tue Nov 25 08:28:24 2014 -0500
+++ b/tools/effectiveT3/README.rst	Wed Aug 05 11:04:42 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for EffectiveT3 v1.0.1
 =====================================
 
-This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -86,7 +86,9 @@
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
 v0.0.13 - Relax unit test to allow for small floating point score difference.
         - Tool definition now embeds citation information.
-        - Fixed error handling in ``effectiveT3.py``.
+v0.0.14 - Fixed error handling in ``effectiveT3.py``.
+v0.0.15 - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -99,24 +101,33 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+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)::
 
-    $ tar -czf effectiveT3.tar.gz tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular
+    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/
+    ...
 
+or::
 
-Check this worked::
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/
+    ...
+
+To just build and check the tar ball, use::
 
-    $ tar -tzf effectiveT3.tar.gz
-    tools/effectiveT3/README.rst
-    tools/effectiveT3/effectiveT3.xml
-    tools/effectiveT3/effectiveT3.py
-    tools/effectiveT3/tool_dependencies.xml
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/effectiveT3/
+    ...
+    $ tar -tzf shed_upload.tar.gz
     tool-data/effectiveT3.loc.sample
+    test-data/empty.fasta
+    test-data/empty_effectiveT3.tabular
     test-data/four_human_proteins.fasta
     test-data/four_human_proteins.effectiveT3.tabular
-    test-data/empty.fasta
-    test-data/empty_effectiveT3.tabular
+    tool-data/effectiveT3.loc.sample
+    tools/effectiveT3/README.rst
+    tools/effectiveT3/effectiveT3.py
+    tools/effectiveT3/effectiveT3.xml
+    tools/effectiveT3/tool_dependencies.xml
 
 
 Licence (MIT)

--- a/tools/effectiveT3/effectiveT3.py	Tue Nov 25 08:28:24 2014 -0500
+++ b/tools/effectiveT3/effectiveT3.py	Wed Aug 05 11:04:42 2015 -0400
@@ -21,25 +21,25 @@
 
 if "-v" in sys.argv or "--version" in sys.argv:
     # TODO - Get version of the JAR file dynamically?
-    print("Wrapper v0.0.13, TTSS_GUI-1.0.1.jar")
+    print("Wrapper v0.0.14, TTSS_GUI-1.0.1.jar")
     sys.exit(0)
 
-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) != 5:
-   stop_err("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
+   sys_exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
 
 model, threshold, fasta_file, tabular_file = sys.argv[1:]
 
 if not os.path.isfile(fasta_file):
-   stop_err("Input FASTA file not found: %s" % fasta_file)
+   sys_exit("Input FASTA file not found: %s" % fasta_file)
 
 if threshold not in ["selective", "sensitive"] \
 and not threshold.startswith("cutoff="):
-   stop_err("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
+   sys_exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
 
 def clean_tabular(raw_handle, out_handle):
     """Clean up Effective T3 output to make it tabular."""
@@ -63,7 +63,7 @@
             else:
                 id, descr = id_descr.split("; ",1)
         except ValueError:
-            stop_err("Problem parsing line:\n%s\n" % line)
+            sys_exit("Problem parsing line:\n%s\n" % line)
         parts = [s.strip() for s in [id, descr, score, effective]]
         out_handle.write("\t".join(parts) + "\n")
         count += 1
@@ -79,25 +79,25 @@
     try:
         child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except Exception, err:
-        stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+        sys_exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
     # Use .communicate as can get deadlocks with .wait(),
     stdout, stderr = child.communicate()
     return_code = child.returncode
     if return_code:
         cmd_str= " ".join(cmd)  # doesn't quote spaces etc
         if stderr and stdout:
-            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
+            sys_exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
         else:
-            stop_err("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
+            sys_exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
 
 if not os.path.isdir(effectiveT3_dir):
-    stop_err("Effective T3 folder not found: %r" % effectiveT3_dir)
+    sys_exit("Effective T3 folder not found: %r" % effectiveT3_dir)
 
 if not os.path.isfile(effectiveT3_jar):
-    stop_err("Effective T3 JAR file not found: %r" % effectiveT3_jar)
+    sys_exit("Effective T3 JAR file not found: %r" % effectiveT3_jar)
 
 if not os.path.isdir(os.path.join(effectiveT3_dir, "module")):
-    stop_err("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module"))
+    sys_exit("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module"))
 
 effectiveT3_model = os.path.join(effectiveT3_dir, "module", model)
 if not os.path.isfile(effectiveT3_model):
@@ -105,7 +105,7 @@
                      % (os.path.join(effectiveT3_dir, "module"),
                         ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module")))))
     sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar)
-    stop_err("Effective T3 model JAR file not found: %r" % effectiveT3_model)
+    sys_exit("Effective T3 model JAR file not found: %r" % effectiveT3_model)
 
 # We will have write access whereever the output should be,
 temp_file = os.path.abspath(tabular_file + ".tmp")
@@ -125,12 +125,12 @@
     # Must run from directory above the module subfolder:
     os.chdir(effectiveT3_dir)
 except:
-    stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir)
+    sys_exit("Could not change to Effective T3 folder: %s" % effectiveT3_dir)
 
 run(cmd)
 
 if not os.path.isfile(temp_file):
-   stop_err("ERROR - No output file from Effective T3")
+   sys_exit("ERROR - No output file from Effective T3")
 
 out_handle = open(tabular_file, "w")
 out_handle.write("#ID\tDescription\tScore\tEffective\n")
@@ -149,4 +149,4 @@
 
 if count and count==errors:
    # Galaxy will still  allow them to see the output file
-   stop_err("All your sequences gave an error code")
+   sys_exit("All your sequences gave an error code")

--- a/tools/effectiveT3/effectiveT3.xml	Tue Nov 25 08:28:24 2014 -0500
+++ b/tools/effectiveT3/effectiveT3.xml	Wed Aug 05 11:04:42 2015 -0400
@@ -1,8 +1,13 @@
-<tool id="effectiveT3" name="Effective T3" version="0.0.13">
+<tool id="effectiveT3" name="Effective T3" version="0.0.15">
     <description>Find bacterial effectors in protein sequences</description>
     <requirements>
         <requirement type="package" version="1.0.1">effectiveT3</requirement>
     </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <version_command interpreter="python">effectiveT3.py --version</version_command>
     <command interpreter="python">
 effectiveT3.py $module.fields.path
@@ -12,11 +17,6 @@
   $restrict.type
 #end if
 $fasta_file $tabular_file</command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
         <param name="module" type="select" display="radio" label="Classification module">