Mercurial > repos > bgruening > upload_testing

changeset 34:9f25296ac133

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author bgruening
date Thu, 06 Jun 2013 02:34:27 -0400
parents 6db18ec30d4c
children 7d57dba74532
files osra.py osra.xml readme repository_dependencies.xml test_data/CID_2244.png test_data/CID_2244.sdf tool_dependencies.xml
diffstat 7 files changed, 0 insertions(+), 269 deletions(-) [+]
line wrap: on
line diff
--- a/osra.py	Thu Jun 06 02:33:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-#!usr/bin/env python
-
-import os, sys
-import subprocess
-
-"""
-    OSRA_DATA_FILES is set during the toolshed Installation
-    If it is not set, use the standard configuration of OSRA. 
-    That means we need to delete argument 4-7.
-    That script is a hack, because we do not know the content of OSRA_DATA_FILES at xml evaluation time.
-
-    osra -f $oformat $infile 
-        -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
-        > $outfile
-"""
-
-if not os.path.exists(sys.argv[6]):
-    # OSRA_DATA_FILES path is not set or the spelling file is not existent
-    sys.argv.pop(7) # superatom.txt path
-    sys.argv.pop(6) # -a
-    sys.argv.pop(5) # speling.txt path
-    sys.argv.pop(4) # -l
-
-subprocess.call(sys.argv[1:], stdout=sys.stdout)
-
-
--- a/osra.xml	Thu Jun 06 02:33:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<tool id="osra" name="Molecule recognition" version="0.3">
-    <description>in Images or PDF documents (OSRA)</description>
-    <requirements>
-        <requirement type="package" version="2.0.0">osra</requirement>
-    </requirements>
-    <command interpreter="python">
-        ## OSRA_DATA_FILES is set during the toolshed Installation
-        ## if it is not set, use the standard configuration and hope the best
-        osra.py -f $oformat $infile 
-        -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
-        
-        ## further additions of OSRA parameter should go after -l and -a
-        ## because -l and -a can be removed by the python wrapper
-        
-        &gt; $outfile
-    </command>
-    <inputs>
-        <param format="png,pdf" label="Image or PDF with molecules" name="infile" type="data" />
-        <param label="Output molecule format" name="oformat" type="select">
-            <option value="can">SMILES</option>
-            <option value="sdf">SDF</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data format="sdf" name="outfile" type="data">
-            <change_format>
-                <when format="smi" input="oformat" value="can" />
-            </change_format>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param ftype="png" name="infile" value="CID_2244.png" />
-            <param name="oformat" value="sdf" />
-            <output file="osra_on_CID2244.sdf" ftype="sdf" name="outfile" />
-        </test>
-    </tests>
-    <help>
-
-**What it does**
-
-OSRA detects molecules in images and converts them to standard molecule formats. 
-
-
-    </help>
-</tool>
--- a/readme	Thu Jun 06 02:33:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-OSRA: Optical Structure Recognition Application
-
-OSRA is a utility designed to convert graphical representations of chemical 
-structures, as they appear in journal articles, patent documents, textbooks, 
-trade magazines etc., into SMILES (Simplified Molecular Input Line Entry 
-Specification - see http://en.wikipedia.org/wiki/SMILES) or 
-SD files - a computer recognizable molecular structure format. 
-OSRA can read a document in any of the over 90 graphical formats parseable by 
-ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate 
-the SMILES or SDF representation of the molecular structure images encountered 
-within that document.
-
-Note that any software designed for optical recognition is unlikely to be 
-perfect, and the output produced might, and probably will, contain errors, 
-so curation by a human knowledgeable in chemical structures is highly recommended.
-
-http://cactus.nci.nih.gov/osra/
-
-The wrapper comes with an automatic installation of all dependencies through the
-galaxy toolshed.
--- a/repository_dependencies.xml	Thu Jun 06 02:33:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository changeset_revision="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    
-</repositories>
Binary file test_data/CID_2244.png has changed
--- a/test_data/CID_2244.sdf	Thu Jun 06 02:33:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-2244
-  -OEChem-05151212332D
-
- 21 21  0     0  0  0  0  0  0999 V2000
-    3.7320   -0.0600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    6.3301    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    4.5981    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    2.8660   -1.5600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    4.5981   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4641   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    4.5981   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.3301   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4641   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.3301   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4641    0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.8660   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.0000   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    4.0611   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    6.8671   -0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4641   -2.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    6.8671   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    2.3100    0.4769    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    1.4631    0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    1.6900   -0.5969    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    6.3301    2.0600    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-  1  5  1  0  0  0  0
-  1 12  1  0  0  0  0
-  2 11  1  0  0  0  0
-  2 21  1  0  0  0  0
-  3 11  2  0  0  0  0
-  4 12  2  0  0  0  0
-  5  6  1  0  0  0  0
-  5  7  2  0  0  0  0
-  6  8  2  0  0  0  0
-  6 11  1  0  0  0  0
-  7  9  1  0  0  0  0
-  7 14  1  0  0  0  0
-  8 10  1  0  0  0  0
-  8 15  1  0  0  0  0
-  9 10  2  0  0  0  0
-  9 16  1  0  0  0  0
- 10 17  1  0  0  0  0
- 12 13  1  0  0  0  0
- 13 18  1  0  0  0  0
- 13 19  1  0  0  0  0
- 13 20  1  0  0  0  0
-M  END
-> <PUBCHEM_COMPOUND_CID>
-2244
-
-> <PUBCHEM_COMPOUND_CANONICALIZED>
-1
-
-> <PUBCHEM_CACTVS_COMPLEXITY>
-212
-
-> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
-4
-
-> <PUBCHEM_CACTVS_HBOND_DONOR>
-1
-
-> <PUBCHEM_CACTVS_ROTATABLE_BOND>
-3
-
-> <PUBCHEM_CACTVS_SUBSKEYS>
-AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA==
-
-> <PUBCHEM_IUPAC_OPENEYE_NAME>
-2-acetoxybenzoic acid
-
-> <PUBCHEM_IUPAC_CAS_NAME>
-2-acetyloxybenzoic acid
-
-> <PUBCHEM_IUPAC_NAME>
-2-acetyloxybenzoic acid
-
-> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
-2-acetyloxybenzoic acid
-
-> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
-2-acetoxybenzoic acid
-
-> <PUBCHEM_IUPAC_INCHI>
-InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
-
-> <PUBCHEM_IUPAC_INCHIKEY>
-BSYNRYMUTXBXSQ-UHFFFAOYSA-N
-
-> <PUBCHEM_XLOGP3>
-1.2
-
-> <PUBCHEM_EXACT_MASS>
-180.042259
-
-> <PUBCHEM_MOLECULAR_FORMULA>
-C9H8O4
-
-> <PUBCHEM_MOLECULAR_WEIGHT>
-180.15742
-
-> <PUBCHEM_OPENEYE_CAN_SMILES>
-CC(=O)OC1=CC=CC=C1C(=O)O
-
-> <PUBCHEM_OPENEYE_ISO_SMILES>
-CC(=O)OC1=CC=CC=C1C(=O)O
-
-> <PUBCHEM_CACTVS_TPSA>
-63.6
-
-> <PUBCHEM_MONOISOTOPIC_WEIGHT>
-180.042259
-
-> <PUBCHEM_TOTAL_CHARGE>
-0
-
-> <PUBCHEM_HEAVY_ATOM_COUNT>
-13
-
-> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
-0
-
-> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
-0
-
-> <PUBCHEM_BOND_DEF_STEREO_COUNT>
-0
-
-> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
-0
-
-> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
-0
-
-> <PUBCHEM_COMPONENT_COUNT>
-1
-
-> <PUBCHEM_CACTVS_TAUTO_COUNT>
-1
-
-> <PUBCHEM_COORDINATE_TYPE>
-1
-5
-255
-
-> <PUBCHEM_BONDANNOTATIONS>
-5  6  8
-5  7  8
-6  8  8
-7  9  8
-8  10  8
-9  10  8
-
-$$$$
-
--- a/tool_dependencies.xml	Thu Jun 06 02:33:42 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="fastqc_dist_0_10_1" version="0.10.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>../FastQC</source_directory>
-                    <destination_directory>$INSTALL_DIR/fastqc_dist</destination_directory>
-                </action>                
-                <action type="shell_command">chmod ugo+x $INSTALL_DIR/fastqc_dist/fastqc</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/fastqc_dist</environment_variable>
-                </action>
-            </actions>
-        </install>
-    </package>
-</tool_dependency>