changeset 0:18eb78773d87 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mol2gspan.py	Tue Oct 29 11:15:59 2013 -0400
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+
+"""
+    Converts a SD-file to a GSPAN file.
+"""
+
+
+import os, sys
+import argparse
+
+def main( args ):
+
+    begin = False
+    iid = 0
+    graph_counter = 1
+
+    for line in args.infile:
+        if line.rstrip():
+            if line.strip().endswith('END'):
+                begin = False
+            elif line.strip() == '$$$$':
+                graph_counter += 1
+                iid = 0
+            else:
+                # found header line, like:  21 21  0  0  0  0  0  0  0  0999 V2000
+                if len(line.split()) >= 5 and line.split()[-1] == 'V2000':
+                    args.outfile.write('t # id %s\n' % graph_counter)
+                    begin=True
+                    continue
+                # connection or coordinate/atom table
+                if len(line.split()) >= 4 and begin:
+                    # coordinate/atom table
+                    if not line.startswith('M'):
+                        if line.split()[3].isalpha() or line.split()[3] == '*':
+                            args.outfile.write( 'v %s %s \n' % (iid, line.split()[3]) )
+                            iid += 1
+                        else:
+                            #connection table
+                            id, node, edge, trash = line.split(None, 3)
+                            args.outfile.write( 'e %s %s %s\n' % ( int(id) - 1 , int(node) -1, edge ) )
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--infile', nargs='?', type=argparse.FileType('r'),
+        default=sys.stdin, help="Specify one or more input files")
+    parser.add_argument('--outfile', type=argparse.FileType('w'),
+        default=sys.stdout, help="Specify one output file")
+    args = parser.parse_args()
+    main( args )

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mol2gspan.xml	Tue Oct 29 11:15:59 2013 -0400
@@ -0,0 +1,41 @@
+<tool id="bg_mol2gspan" name="Molecule to gSpan" version="0.1">
+    <description>converter</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+        <requirement type="set_environment">MOL2GSPAN_SCRIPT_PATH</requirement>
+    </requirements>
+    <command>
+
+        #if $infile.ext == 'sdf':
+            python \$MOL2GSPAN_SCRIPT_PATH/mol2gspan.py --infile $infile --outfile $outfile
+
+        #else:
+            obabel -i $infile.ext -o sdf $infile ---errorlevel 1 | python \$MOL2GSPAN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $outfile
+
+        #end if
+
+    </command>
+    <inputs>
+        <param format="smi,sdf,mol,inchi,mol2" name="infile" type="data" 
+            label="Input molecules" help=""/>
+    </inputs>
+    <outputs>
+        <data format="gspan" name="outfile" label="gSpan from ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="3_molceuls.sdf" />
+            <output name="outfile" file="3_molecules.gspan" />
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What it does** 
+
+That converter will convert arbitratry molecule files to the gSpan format.
+
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Tue Oct 29 11:15:59 2013 -0400
@@ -0,0 +1,48 @@
+Galaxy wrapper for mol2gspan
+============================
+
+This wrapper is copyright 2013 by Björn Grüning.
+
+This is a wrapper for the command line tool of mol2gspan.
+
+
+
+
+Installation
+============
+
+The recommended installation is by means of the toolshed_.
+If you need to install it manually here is a short introduction.
+
+.. _toolshed: http://toolshed.g2.bx.psu.edu/view/bgruening/molecule2gspan
+
+
+
+History
+=======
+
+- v0.1: Initial public release
+
+
+=============
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Tue Oct 29 11:15:59 2013 -0400
@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format) and the EDeN datatypes.">
+    <repository changeset_revision="8714f927a6ee" name="molecule_datatypes" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="59b3b6ce10bb" name="eden_toolbox" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 29 11:15:59 2013 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="openbabel" version="2.3.2">
+        <repository changeset_revision="7601c962048a" name="package_openbabel_2_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="MOL2GSPAN_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+</tool_dependency>