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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go commit 0c82b9ef284c686cbffd30582d2586e4fb52881e"
author peterjc
date Wed, 09 Sep 2020 15:01:39 +0000
parents 05eef6b222af
children
files tools/blast2go/README.rst tools/blast2go/blast2go.py tools/blast2go/blast2go.xml tools/blast2go/massage_xml_for_blast2go.py tools/blast2go/repository_dependencies.xml tools/blast2go/tool_dependencies.xml
diffstat 6 files changed, 90 insertions(+), 116 deletions(-) [+]
line wrap: on
line diff
--- a/tools/blast2go/README.rst	Fri May 15 06:01:16 2015 -0400
+++ b/tools/blast2go/README.rst	Wed Sep 09 15:01:39 2020 +0000
@@ -1,7 +1,7 @@
 Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
 ===================================================
 
-This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2011-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -24,22 +24,22 @@
 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 S. Geotz et al. (2008).
 High-throughput functional annotation and data mining with the Blast2GO suite.
 Nucleic Acids Res. 36(10):3420-3435.
-http://dx.doi.org/10.1093/nar/gkn176
+https://doi.org/10.1093/nar/gkn176
 
 A. Conesa and S. Geotz (2008).
 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
 International Journal of Plant Genomics. 619832.
-http://dx.doi.org/10.1155/2008/619832
+https://doi.org/10.1155/2008/619832
 
 A. Conesa et al. (2005).
 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
 Bioinformatics 21:3674-3676.
-http://dx.doi.org/10.1093/bioinformatics/bti610
+https://doi.org/10.1093/bioinformatics/bti610
 
 See also http://www.blast2go.com/
 
@@ -166,6 +166,13 @@
         - Tool definition now embeds citation information.
 v0.0.10 - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.11 - Fix parameter help text which was not being displayed.
+        - PEP8 style updates to the Python script (internal change only).
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
+        - Python 3 compatible syntax.
+        - Record ``b2g4pipe_v2.5.zip`` SHA256 checksum, and download this via
+          the Galaxy pacakge cache.
 ======= ======================================================================
 
 
@@ -183,19 +190,19 @@
 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/galaxy_blast/tools/blast2go/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast2go/
     ...
 
 or::
 
-    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast2go/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blast2go/
     ...
 
 To just build and check the tar ball, use::
 
     $ planemo shed_upload --tar_only  ~/repositories/galaxy_blast/tools/blast2go/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/blastp_sample.blast2go.tabular
     test-data/blastp_sample.xml
     tool-data/blast2go.loc.sample
--- a/tools/blast2go/blast2go.py	Fri May 15 06:01:16 2015 -0400
+++ b/tools/blast2go/blast2go.py	Wed Sep 09 15:01:39 2020 +0000
@@ -26,61 +26,65 @@
 This script is under version control here:
 https://github.com/peterjc/galaxy_blast/tree/master/blast2go
 """
-import sys
+
+from __future__ import print_function
+
 import os
 import subprocess
+import sys
 
-#You may need to edit this to match your local setup,
+# You may need to edit this to match your local setup,
 blast2go_dir = os.environ.get("B2G4PIPE", "/opt/b2g4pipe_v2.5/")
 blast2go_jar = os.path.join(blast2go_dir, "blast2go.jar")
 
-def stop_err(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)
 
 try:
     from massage_xml_for_blast2go import prepare_xml
 except ImportError:
-    stop_err("Missing sister file massage_xml_for_blast2go.py")
+    sys.exit("Missing sister file massage_xml_for_blast2go.py")
 
 if len(sys.argv) != 4:
-    stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
+    sys.exit(
+        "Require three arguments: XML filename, "
+        "properties filename, output tabular filename"
+    )
 
 xml_file, prop_file, tabular_file = sys.argv[1:]
 
-#We should have write access here:
+# We should have write access here:
 tmp_xml_file = tabular_file + ".tmp.xml"
 
 if not os.path.isfile(blast2go_jar):
-    stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
+    sys.exit("Blast2GO JAR file not found: %s" % blast2go_jar)
 
 if not os.path.isfile(xml_file):
-    stop_err("Input BLAST XML file not found: %s" % xml_file)
+    sys.exit("Input BLAST XML file not found: %s" % xml_file)
 
 if not os.path.isfile(prop_file):
     tmp = os.path.join(os.path.split(blast2go_jar)[0], prop_file)
     if os.path.isfile(tmp):
-        #The properties file seems to have been given relative to the JAR
+        # The properties file seems to have been given relative to the JAR
         prop_file = tmp
     else:
-        stop_err("Blast2GO configuration file not found: %s" % prop_file)
+        sys.exit("Blast2GO configuration file not found: %s" % prop_file)
     del tmp
 
 
 def run(cmd):
-    #Avoid using shell=True when we call subprocess to ensure if the Python
-    #script is killed, so too is the child process.
+    """Run the given command line string via subprocess."""
+    # Avoid using shell=True when we call subprocess to ensure if the Python
+    # script is killed, so too is the child process.
     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))
-    #Use .communicate as can get deadlocks with .wait(),
+        child = subprocess.Popen(
+            cmd, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        )
+    except Exception as err:
+        sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
     stdout, stderr = child.communicate()
     return_code = child.returncode
 
-    #keep stdout minimal as shown prominently in Galaxy
-    #Record it in case a silent error needs diagnosis
+    # keep stdout minimal as shown prominently in Galaxy
+    # Record it in case a silent error needs diagnosis
     if stdout:
         sys.stderr.write("Standard out:\n%s\n\n" % stdout)
     if stderr:
@@ -90,14 +94,14 @@
     if return_code:
         cmd_str = " ".join(cmd)
         error_msg = "Return code %i from command:\n%s" % (return_code, cmd_str)
-    elif "Database or network connection (timeout) error" in stdout+stderr:
+    elif "Database or network connection (timeout) error" in stdout + stderr:
         error_msg = "Database or network connection (timeout) error"
-    elif "Annotation of 0 seqs with 0 annots finished." in stdout+stderr:
+    elif "Annotation of 0 seqs with 0 annots finished." in stdout + stderr:
         error_msg = "No sequences processed!"
 
     if error_msg:
-        print error_msg
-        stop_err(error_msg)
+        print(error_msg)
+        sys.exit(error_msg)
 
 
 blast2go_classpath = os.path.split(blast2go_jar)[0]
@@ -105,30 +109,37 @@
 blast2go_classpath = "%s/*:%s/ext/*:" % (blast2go_classpath, blast2go_classpath)
 
 prepare_xml(xml_file, tmp_xml_file)
-#print "XML file prepared for Blast2GO"
+# print "XML file prepared for Blast2GO"
 
-#We will have write access wherever the output should be,
-#so we'll ask Blast2GO to use that as the stem for its output
-#(it will append .annot to the filename)
-cmd = ["java", "-cp", blast2go_classpath, "es.blast2go.prog.B2GAnnotPipe",
-       "-in", tmp_xml_file,
-       "-prop", prop_file,
-       "-out", tabular_file, #Used as base name for output files
-       "-annot", # Generate *.annot tabular file
-       #NOTE: For v2.3.5 must use -a, for v2.5 must use -annot instead
-       #"-img", # Generate images, feature not in v2.3.5
-       ]
-#print " ".join(cmd)
+# We will have write access wherever the output should be,
+# so we'll ask Blast2GO to use that as the stem for its output
+# (it will append .annot to the filename)
+cmd = [
+    "java",
+    "-cp",
+    blast2go_classpath,
+    "es.blast2go.prog.B2GAnnotPipe",
+    "-in",
+    tmp_xml_file,
+    "-prop",
+    prop_file,
+    "-out",
+    tabular_file,  # Used as base name for output files
+    "-annot",  # Generate *.annot tabular file
+    # NOTE: For v2.3.5 must use -a, for v2.5 must use -annot instead
+    # "-img", # Generate images, feature not in v2.3.5
+]
+# print " ".join(cmd)
 run(cmd)
 
-#Remove the temp XML file
+# Remove the temp XML file
 os.remove(tmp_xml_file)
 
 out_file = tabular_file + ".annot"
 if not os.path.isfile(out_file):
-    stop_err("ERROR - No output annotation file from Blast2GO")
+    sys.exit("ERROR - No output annotation file from Blast2GO")
 
-#Move the output file where Galaxy expects it to be:
+# Move the output file where Galaxy expects it to be:
 os.rename(out_file, tabular_file)
 
-print "Done"
+print("Done")
--- a/tools/blast2go/blast2go.xml	Fri May 15 06:01:16 2015 -0400
+++ b/tools/blast2go/blast2go.xml	Wed Sep 09 15:01:39 2020 +0000
@@ -1,19 +1,14 @@
-<tool id="blast2go" name="Blast2GO" version="0.0.10">
+<tool id="blast2go" name="Blast2GO" version="0.0.11" profile="16.10">
     <description>Maps BLAST results to GO annotation terms</description>
     <requirements>
         <requirement type="package" version="2.5">b2g4pipe</requirement>
     </requirements>
-    <stdio>
-        <!-- Wrapper ensures anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <command interpreter="python">
-        blast2go.py "${xml}" "${prop.fields.path}" "${tab}"
+    <command detect_errors="aggressive">
+python $__tool_directory__/blast2go.py '$xml' '${prop.fields.path}' '$tab'
     </command>
     <inputs>
-        <param name="xml" type="data" format="blastxml" label="BLAST XML results" description="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." /> 
-        <param name="prop" type="select" label="Blast2GO settings" description="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database.">
+        <param name="xml" type="data" format="blastxml" label="BLAST XML results" help="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." />
+        <param name="prop" type="select" label="Blast2GO settings" help="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database.">
              <options from_file="blast2go.loc">
                  <column name="value" index="0"/>
                  <column name="name" index="1"/>
@@ -92,22 +87,22 @@
 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 S. Götz et al. (2008).
 High-throughput functional annotation and data mining with the Blast2GO suite.
 Nucleic Acids Res. 36(10):3420–3435.
-http://dx.doi.org/10.1093/nar/gkn176
+https://doi.org/10.1093/nar/gkn176
 
 A. Conesa and S. Götz (2008).
 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
 International Journal of Plant Genomics. 619832.
-http://dx.doi.org/10.1155/2008/619832
+https://doi.org/10.1155/2008/619832
 
 A. Conesa et al. (2005).
 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
 Bioinformatics 21:3674-3676.
-http://dx.doi.org/10.1093/bioinformatics/bti610
+https://doi.org/10.1093/bioinformatics/bti610
 
 See also http://www.blast2go.com/
 
--- a/tools/blast2go/massage_xml_for_blast2go.py	Fri May 15 06:01:16 2015 -0400
+++ b/tools/blast2go/massage_xml_for_blast2go.py	Wed Sep 09 15:01:39 2020 +0000
@@ -14,18 +14,15 @@
 
 This script is called from my Galaxy wrapper for Blast2GO for pipelines,
 available from the Galaxy Tool Shed here:
-http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go 
+http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
 
 This script is under version control here:
 https://github.com/peterjc/galaxy_blast/tree/master/blast2go
 """
-import sys
-import os
 
-def stop_err(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)
+import os
+import sys
+
 
 def prepare_xml(original_xml, mangled_xml):
     """Reformat BLAST XML to suit Blast2GO.
@@ -44,8 +41,8 @@
     while True:
         line = in_handle.readline()
         if not line:
-            #No hits?
-            stop_err("Problem with XML file?")
+            # No hits?
+            sys.exit("Problem with XML file?")
         if line.strip() == "<Iteration>":
             break
         header += line
@@ -56,7 +53,7 @@
         print("BLASTP output identified")
     else:
         in_handle.close()
-        stop_err("Expect BLASTP or BLASTX output")
+        sys.exit("Expect BLASTP or BLASTX output")
 
     out_handle = open(mangled_xml, "w")
     out_handle.write(header)
@@ -67,10 +64,10 @@
         if not line:
             break
         elif line.strip() == "<Iteration>":
-           #Insert footer/header
-           out_handle.write(footer)
-           out_handle.write(header)
-           count += 1
+            # Insert footer/header
+            out_handle.write(footer)
+            out_handle.write(header)
+            count += 1
         out_handle.write(line)
 
     out_handle.close()
@@ -81,11 +78,11 @@
 if __name__ == "__main__":
     # Run the conversion...
     if len(sys.argv) != 3:
-        stop_err("Require two arguments: XML input filename, XML output filename")
+        sys.exit("Require two arguments: XML input filename, XML output filename")
 
     xml_file, out_xml_file = sys.argv[1:]
 
     if not os.path.isfile(xml_file):
-        stop_err("Input BLAST XML file not found: %s" % xml_file)
+        sys.exit("Input BLAST XML file not found: %s" % xml_file)
 
     prepare_xml(xml_file, out_xml_file)
--- a/tools/blast2go/repository_dependencies.xml	Fri May 15 06:01:16 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Requires BLAST XML and database datatype definitions.">
-    <repository changeset_revision="da92fef90117" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>
--- a/tools/blast2go/tool_dependencies.xml	Fri May 15 06:01:16 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="b2g4pipe" version="2.5">
-        <install version="1.0">
-            <actions>
-                <!-- If used, download_by_url must be the first action -->	
-                <!-- The ZIP file decompresses to give a folder b2g4pipe -->
-                <action type="download_by_url">http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip</action>
-		<!-- Galaxy moves into the unzipped folder b2g4pipe -->
-                <action type="shell_command">
-cp b2gPipe.properties Spain_2012_August.properties &amp;&amp;
-sed -i "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_aug12/g" Spain_2012_August.properties &amp;&amp;
-sed -i "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2012_August.properties
-                </action>
-                <action type="shell_command">
-cp b2gPipe.properties Spain_2011_June.properties &amp;&amp;
-sed -i "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_jun11/g" Spain_2011_June.properties &amp;&amp;
-sed -i "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2011_June.properties
-                </action>
-                <action type="move_directory_files"><source_directory>.</source_directory><destination_directory>$INSTALL_DIR/</destination_directory></action>
-                <!-- Set environment variable $B2G4PIPE so Python script knows where to look -->
-                <action type="set_environment">
-                    <environment_variable name="B2G4PIPE" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Downloads b2g4pipe v2.5
-        </readme>
-    </package>
-</tool_dependency>
-