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Changeset 2:fb591fc7241c (2013-06-20)

Previous changeset 1:7a74818e0eeb (2013-06-20) Next changeset 3:679a4b0041a4 (2013-06-20)

Commit message:
Improved some datatype handling

modified:
peptide_shaker.xml

added:
datatypes_conf.xml
dbtoolkit-4.2/LICENSE-2.0.txt
dbtoolkit-4.2/dbtoolkit-4.2.jar
dbtoolkit-4.2/lib/jargs-1.0.jar
dbtoolkit-4.2/lib/log4j-1.2.12.jar
dbtoolkit-4.2/lib/utilities-3.8.7.jar
peptideshaker.py
reverse.py
reverse.xml

removed:
galaxyp-toolshed-peptideshaker

diff -r 7a74818e0eeb -r fb591fc7241c datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Thu Jun 20 11:02:36 2013 -0400

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<datatypes>
+  <datatype_files>
+    <datatype_file name="peptideshaker.py"/>
+  </datatype_files>
+  <registration>
+    <datatype extension="cps" type="galaxy.datatypes.peptideshaker:Cps" display_in_upload="true" />
+  </registration>
+</datatypes>

diff -r 7a74818e0eeb -r fb591fc7241c dbtoolkit-4.2/LICENSE-2.0.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dbtoolkit-4.2/LICENSE-2.0.txt Thu Jun 20 11:02:36 2013 -0400

[

b'@@ -0,0 +1,202 @@\n+\n+ Apache License\n+ Version 2.0, January 2004\n+ http://www.apache.org/licenses/\n+\n+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n+\n+ 1. Definitions.\n+\n+ "License" shall mean the terms and conditions for use, reproduction,\n+ and distribution as defined by Sections 1 through 9 of this document.\n+\n+ "Licensor" shall mean the copyright owner or entity authorized by\n+ the copyright owner that is granting the License.\n+\n+ "Legal Entity" shall mean the union of the acting entity and all\n+ other entities that control, are controlled by, or are under common\n+ control with that entity. 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diff -r 7a74818e0eeb -r fb591fc7241c dbtoolkit-4.2/dbtoolkit-4.2.jar

Binary file dbtoolkit-4.2/dbtoolkit-4.2.jar has changed

diff -r 7a74818e0eeb -r fb591fc7241c dbtoolkit-4.2/lib/jargs-1.0.jar

Binary file dbtoolkit-4.2/lib/jargs-1.0.jar has changed

diff -r 7a74818e0eeb -r fb591fc7241c dbtoolkit-4.2/lib/log4j-1.2.12.jar

Binary file dbtoolkit-4.2/lib/log4j-1.2.12.jar has changed

diff -r 7a74818e0eeb -r fb591fc7241c dbtoolkit-4.2/lib/utilities-3.8.7.jar

Binary file dbtoolkit-4.2/lib/utilities-3.8.7.jar has changed

diff -r 7a74818e0eeb -r fb591fc7241c galaxyp-toolshed-peptideshaker
--- a/galaxyp-toolshed-peptideshaker Thu Jun 20 10:53:16 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r 7a74818e0eeb -r fb591fc7241c peptide_shaker.xml
--- a/peptide_shaker.xml Thu Jun 20 10:53:16 2013 -0400
+++ b/peptide_shaker.xml Thu Jun 20 11:02:36 2013 -0400

@@ -4,6 +4,9 @@
     Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
   </description>
   <command>
+    #from datetime import datetime
+    #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s")
+    #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")
     mkdir spectra;
     mkdir output;
     mkdir output_reports;
@@ -45,8 +48,8 @@
     #end if
     -db $input_database;
     PeptideShakerCLI \
-    -experiment 'Galaxy Experiment' \
-    -sample 'Sample' \
+    -experiment '$exp_str' \
+    -sample '$samp_str' \
     -replicate 1 \
     -spectrum_files \$cwd/spectra \
     -identification_files \$cwd/output \
@@ -210,12 +213,14 @@
   <help>
**What it does**

+Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the result via PeptideShaker.
+
------

**Citation**

For the underlying tool, please cite `TODO`

-If you use this tool in Galaxy, please cite TODO
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker
   </help>
</tool>

diff -r 7a74818e0eeb -r fb591fc7241c peptideshaker.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peptideshaker.py Thu Jun 20 11:02:36 2013 -0400

@@ -0,0 +1,8 @@
+from galaxy.datatypes.binary import Binary
+
+
+class Cps(Binary):
+ """Class describing a PeptideShaker CPS files"""
+ file_ext = "cps"
+
+Binary.register_unsniffable_binary_ext('cps')

diff -r 7a74818e0eeb -r fb591fc7241c reverse.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reverse.py Thu Jun 20 11:02:36 2013 -0400

[

@@ -0,0 +1,50 @@
+from os.path import dirname, join, abspath
+import sys
+from optparse import OptionParser
+from ConfigParser import SafeConfigParser
+import subprocess
+
+DEBUG = False
+
+
+def main():
+    (options, args) = _parse_args()
+    format_args = (options.input, options.output)
+    _run_shell("cat '%s' > '%s'" % format_args)
+    _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % \
+                       format_args)
+
+
+def _run_shell(command):
+    if DEBUG:
+        print "Running shell command %s" % command
+    _exec(command)
+
+
+def _run_dbtoolkit(java_class, args):
+    command_prefix = "java -cp %s" % _dbtoolkit_jar_path()
+    _exec("%s %s %s" % (command_prefix, java_class, args))
+
+
+def _dbtoolkit_jar_path():
+    py_path = __file__
+    jar_path = join(dirname(py_path), "dbtoolkit-4.2", "dbtoolkit-4.2.jar")
+    return jar_path
+
+def _exec(command):
+    proc = subprocess.Popen(args=command, shell=True)
+    return_code = proc.wait()
+    if return_code != 0:
+        print "Error executing command [%s], return code is %d" % (command, return_code)
+        sys.exit(return_code)
+
+
+def _parse_args():
+    parser = OptionParser()
+    parser.add_option("-i", "--input")
+    parser.add_option("-o", "--output")
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    main()

diff -r 7a74818e0eeb -r fb591fc7241c reverse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reverse.xml Thu Jun 20 11:02:36 2013 -0400

@@ -0,0 +1,32 @@
+<tool id="compomics_reverse" name="Create Target-Decoy Database" version="0.1.0">
+  <description>Creates a target-decoy database for use with Peptide Shaker</description>
+
+  <requirements>
+  </requirements>
+
+  <command interpreter="python">reverse.py --input='$input' --output='$output'</command>
+
+  <inputs>
+    <param format="fasta" name="input" type="data" label="FASTA Input" />
+  </inputs>
+
+  <outputs>
+    <data format="fasta" name="output" />
+  </outputs>
+
+  <help>
+**What it does**
+
+Given an input database, this tool will produce a target-decoy
+database in the format required by PeptideShaker using dbtoolkit.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Martens et al. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (2005) vol. 21 (17) pp. 3584-5`.
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker .
+
+  </help>
+</tool>