changeset 0:156ef965340e draft default tip

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author galaxyp
date Wed, 08 Oct 2014 13:46:58 -0400
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files COPYING README.md datatypes_conf.xml protxml2html_wrapper.py protxml_datatypes.py protxml_to_xls.xml repository_dependencies.xml test-data/.gitkeep tool-data/.gitkeep tool_dependencies.xml
diffstat 8 files changed, 333 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Wed Oct 08 13:46:58 2014 -0400
@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Oct 08 13:46:58 2014 -0400
@@ -0,0 +1,55 @@
+GalaxyP - ProtXML to Tabular
+============================
+
+* Home: <https://bitbucket.org/galaxyp/protxml_to_tabular>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/protxml_to_tabular>
+* Tool ID: `protxml_to_tabular`
+
+
+Description
+-----------
+
+Converts ProtXML to Tabular using protxml2html from the the TransProteomicPipeline.
+
+See:
+
+* <http://www.proteomecenter.org/software.php>
+* <http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP>
+* <https://en.wikipedia.org/wiki/Trans-Proteomic_Pipeline>
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
+
+<https://bitbucket.org/galaxyp/galaxyp>
+
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+Contributing
+------------
+
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out.
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* Cody Wang
+* Fred Sadler
+* John Chilton <jmchilton@gmail.com>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Wed Oct 08 13:46:58 2014 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<datatypes>
+  <datatype_files>
+    <datatype_file name="protxml_datatypes.py"/>
+  </datatype_files>
+  <registration>
+    <datatype extension="protxml.tsv" type="galaxy.datatypes.protxml_datatypes:ProtXmlReport" display_in_upload="true" />
+  </registration>
+</datatypes>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protxml2html_wrapper.py	Wed Oct 08 13:46:58 2014 -0400
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil
+import subprocess
+import re
+from os.path import basename
+import logging
+
+assert sys.version_info[:2] >= ( 2, 6 )
+
+log = logging.getLogger(__name__)
+working_directory = os.getcwd()
+tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name
+tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def read_stderr():
+    stderr = ''
+    if(os.path.exists(tmp_stderr_name)):
+        with open(tmp_stderr_name, 'rb') as tmp_stderr:
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read(buffsize)
+                    if not stderr or len(stderr) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+    return stderr
+
+def execute(command, stdin=None):
+    with open(tmp_stderr_name, 'wb') as tmp_stderr:
+        with open(tmp_stdout_name, 'wb') as tmp_stdout:
+            proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
+            returncode = proc.wait()
+            if returncode != 0:
+                raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
+
+def delete_file(path):
+    if os.path.exists(path):
+        try:
+            os.remove(path)
+        except:
+            pass
+
+def delete_directory(directory):
+    if os.path.exists(directory):
+        try:
+            shutil.rmtree(directory)
+        except:
+            pass
+
+def symlink(source, link_name):
+    import platform
+    if platform.system() == 'Windows':
+        import win32file
+        win32file.CreateSymbolicLink(source, link_name, 1)
+    else:
+        os.symlink(source, link_name)
+
+
+def copy_to_working_directory(data_file, relative_path):
+    if os.path.abspath(data_file) != os.path.abspath(relative_path):
+        shutil.copy(data_file, relative_path)
+    return relative_path
+
+def __main__():
+    run_script()
+
+#ENDTEMPLATE
+
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option("--input")
+    parser.add_option("--export_spreadsheet", action="store_true", dest="export_spreadsheet")
+    parser.set_defaults(export_spreadsheet=False)
+    (options, args) = parser.parse_args()
+
+    copy_to_working_directory(options.input, "input.prot.xml")
+    # Trans-Proteomic Pipeline - bin/protxml2html.pl
+    cmd = "protxml2html.pl -file ./input.prot.xml"
+    if options.export_spreadsheet:
+        cmd = "%s FORMAT EXCEL" % cmd
+    else:
+        cmd = "%s FORMAT HTML" % cmd
+    execute(cmd)
+
+if __name__ == '__main__': __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protxml_datatypes.py	Wed Oct 08 13:46:58 2014 -0400
@@ -0,0 +1,21 @@
+from galaxy.datatypes.tabular import Tabular
+import logging
+
+log = logging.getLogger(__name__)
+
+
+class ProtXmlReport(Tabular):
+    """protxml converted to tabular report"""
+    file_ext = "tsv"
+    comment_lines = 1
+
+    def __init__(self, **kwd):
+        Tabular.__init__( self, **kwd )
+        self.column_names = ["Entry Number", "Group Probability", "Protein", "Protein Link", "Protein Probability", "Percent Coverage", "Number of Unique Peptides", "Total Independent Spectra", "Percent Share of Spectrum ID's", "Description", "Protein Molecular Weight", "Protein Length", "Is Nondegenerate Evidence", "Weight", "Precursor Ion Charge", "Peptide sequence", "Peptide Link", "NSP Adjusted Probability", "Initial Probability", "Number of Total Termini", "Number of Sibling Peptides Bin", "Number of Instances", "Peptide Group Designator", "Is Evidence?"]
+
+    def set_meta( self, dataset, **kwd ):
+        Tabular.set_meta( self, dataset, **kwd )
+
+    #def display_peek( self, dataset ):
+    #    """Returns formated html of peek"""
+    #    return Tabular.make_html_table( self, dataset, column_names=self.column_names )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protxml_to_xls.xml	Wed Oct 08 13:46:58 2014 -0400
@@ -0,0 +1,22 @@
+<tool id="protxml_to_xls" name="Convert ProtXML to Tabular" version="0.1.0">
+  <requirements>
+    <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
+  </requirements>
+
+  <description></description>
+
+  <command interpreter="python">
+    protxml2html_wrapper.py --input=${input} --export_spreadsheet
+  </command>
+
+  <inputs>
+    <param format="prot.xml" name="input" type="data" label="ProtXML Input"/>
+  </inputs>
+
+  <outputs>
+    <data format="protxml.tsv" name="output" from_work_dir="input.prot.xls" />
+  </outputs>
+
+  <help>
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Wed Oct 08 13:46:58 2014 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+  <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Oct 08 13:46:58 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="trans_proteomic_pipeline" version="4.6.3">
+    <repository changeset_revision="0bce36ee6bf2" name="package_tpp_4_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>