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v0.0.11 - Assorted packaging updates (overdue upload)
author peterjc
date Tue, 06 Dec 2022 16:29:50 +0000
parents 887adf823bc0
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, 55 insertions(+), 74 deletions(-) [+]
line wrap: on
line diff
--- a/tools/blast2go/README.rst	Tue Dec 06 16:26:16 2022 +0000
+++ b/tools/blast2go/README.rst	Tue Dec 06 16:29:50 2022 +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/
 
@@ -164,8 +164,16 @@
           of the Blast2GO command line tool. For now b2g4pipe v2.5 is still
           available as a free download.
         - Tool definition now embeds citation information.
-v0.0.10 - Reorder XML elements (internal change only).
+v0.0.10 - Python 3 ready
+        - 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 package cache.
 ======= ======================================================================
 
 
@@ -195,7 +203,7 @@
 
     $ 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	Tue Dec 06 16:26:16 2022 +0000
+++ b/tools/blast2go/blast2go.py	Tue Dec 06 16:29:50 2022 +0000
@@ -26,9 +26,11 @@
 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,
 blast2go_dir = os.environ.get("B2G4PIPE", "/opt/b2g4pipe_v2.5/")
@@ -41,7 +43,10 @@
     sys.exit("Missing sister file massage_xml_for_blast2go.py")
 
 if len(sys.argv) != 4:
-    sys.exit("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:]
 
@@ -65,11 +70,14 @@
 
 
 def run(cmd):
+    """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:
+        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
@@ -91,7 +99,7 @@
         error_msg = "No sequences processed!"
 
     if error_msg:
-        print error_msg
+        print(error_msg)
         sys.exit(error_msg)
 
 
@@ -105,14 +113,21 @@
 # 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
-       ]
+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)
 
@@ -126,4 +141,4 @@
 # 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	Tue Dec 06 16:26:16 2022 +0000
+++ b/tools/blast2go/blast2go.xml	Tue Dec 06 16:29:50 2022 +0000
@@ -1,19 +1,15 @@
-<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>
+        <requirement type="package" version="3.9">python</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 +88,22 @@
 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	Tue Dec 06 16:26:16 2022 +0000
+++ b/tools/blast2go/massage_xml_for_blast2go.py	Tue Dec 06 16:29:50 2022 +0000
@@ -19,8 +19,8 @@
 This script is under version control here:
 https://github.com/peterjc/galaxy_blast/tree/master/blast2go
 """
+import os
 import sys
-import os
 
 
 def prepare_xml(original_xml, mangled_xml):
--- a/tools/blast2go/repository_dependencies.xml	Tue Dec 06 16:26:16 2022 +0000
+++ /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 name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="01b38f20197e"/>
-</repositories>
\ No newline at end of file
--- a/tools/blast2go/tool_dependencies.xml	Tue Dec 06 16:26:16 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +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.bak "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_aug12/g" Spain_2012_August.properties &amp;&amp;
-sed -i.bak "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2012_August.properties
-rm Spain_2012_August.properties.bak
-                </action>
-                <action type="shell_command">
-cp b2gPipe.properties Spain_2011_June.properties &amp;&amp;
-sed -i.bak "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_jun11/g" Spain_2011_June.properties &amp;&amp;
-sed -i.bak "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2011_June.properties
-rm Spain_2011_June.properties.bak
-                </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>
-