# HG changeset patch
# User bgruening
# Date 1446391902 18000
# Node ID 548537fc25775de5350783e6ac389ceb26e28e1d
# Parent  731ad135ddb4af2d45dd795d09a83bfcbc24b326
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty

diff -r 731ad135ddb4 -r 548537fc2577 confab.tar.bz2
Binary file confab.tar.bz2 has changed
diff -r 731ad135ddb4 -r 548537fc2577 confab.xml
--- a/confab.xml	Sun Nov 01 10:28:54 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,142 +0,0 @@
-<tool id="ctb_confab" name="Conformer calculation" version="0.1">
-    <description>for molecules (confab)</description>
-    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
-    <requirements>
-        <requirement type="package" version="1.0.1">confab</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-    confab
-        -i ${infile.ext}
-        -o sdf
-        -r $RMSD
-        -e $energy
-        -c $conformers
-        $first_conformer
-        $infile
-        $outfile 2>&1
-]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
-        <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
-        <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
-        <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
-        <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
-    </inputs>
-    <outputs>
-        <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="infile" value='CID_3033.sdf' ftype='sdf' />
-            <param name='RMSD'  value='0.5' />
-            <param name='energy' value='50.0' />
-            <param name='conformers' value='100000' />
-            <param name='first_conformer' value='-a' />
-            <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
-        </test>
-    </tests>
-<help>
-<![CDATA[
-
-.. class:: infomark
-
-**What this tool does**
-
-Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers.
-
-.. _Confab: https://code.google.com/p/confab/
-
------
-
-.. class:: infomark
-
-**Input**
-
-* Example::
-
-	21.2060    9.9350   63.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
-	21.2410    9.4460   64.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
-	22.0000    8.1250   64.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
-	21.7010    7.3010   65.5120 O   0  0  0  0  0  0  0  0  0  0  0  0
-	23.1180    7.8720   63.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
-	23.4530    8.7270   62.7850 C   0  0  0  0  0  0  0  0  0  0  0  0
-	24.6970    8.4430   61.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
-
-	.......
-
-	1  2  1  0  0  0  0
-	1 11  1  0  0  0  0
-	2  3  1  0  0  0  0
-	3  4  2  0  0  0  0
-	3  5  1  0  0  0  0
-	5  6  2  0  0  0  0
-	6  7  1  0  0  0  0
-
-	RMSD cutoff (in Angstrom)	0.5
-	Energy cutoff (in kcal/mol)	50.0
-	Max number of conformers to test	100000
-	Include the input conformation as the first conformer	False
-
------
-
-.. class:: infomark
-
-**Output**
-
-* Example::
-
-     23 26  0  0  0  0  0  0  0  0999 V2000
-   21.2060    9.9350   63.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
-   21.2410    9.4460   64.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
-   22.0000    8.1250   64.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
-   21.7010    7.3010   65.5120 O   0  0  0  0  0  0  0  0  0  0  0  0
-   23.1180    7.8720   63.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
-   23.4530    8.7270   62.7850 C   0  0  0  0  0  0  0  0  0  0  0  0
-   24.6970    8.4430   61.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
-   24.4490    8.6370   60.4430 C   0  0  0  0  0  0  0  0  0  0  0  0
-   23.7890    9.9970   60.0980 C   0  0  2  0  0  0  0  0  0  0  0  0
-   22.4340   10.0950   60.8720 C   0  0  1  0  0  0  0  0  0  0  0  0
-   22.6140   10.0230   62.4340 C   0  0  1  0  0  0  0  0  0  0  0  0
-   21.6330   11.3540   60.4500 C   0  0  0  0  0  0  0  0  0  0  0  0
-   21.4320   11.4340   58.9110 C   0  0  0  0  0  0  0  0  0  0  0  0
-   22.7860   11.4040   58.1690 C   0  0  1  0  0  0  0  0  0  0  0  0
-   23.4830   10.0600   58.5980 C   0  0  1  0  0  0  0  0  0  0  0  0
-   24.6740    9.9180   57.6180 C   0  0  0  0  0  0  0  0  0  0  0  0
-   24.0720   10.4500   56.2670 C   0  0  0  0  0  0  0  0  0  0  0  0
-   22.7140   11.1490   56.6270 C   0  0  2  0  0  0  0  0  0  0  0  0
-   23.6590   12.6770   58.4540 C   0  0  0  0  0  0  0  0  0  0  0  0
-   23.4270   11.2460   63.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
-   22.3750   12.3880   55.7810 C   0  0  0  0  0  0  0  0  0  0  0  0
-   23.2120   12.8760   55.0520 O   0  0  0  0  0  0  0  0  0  0  0  0
-   21.0090   12.9760   55.8570 C   0  0  0  0  0  0  0  0  0  0  0  0
-
-::
-
-  1  2  1  0  0  0  0
-  1 11  1  0  0  0  0
-  2  3  1  0  0  0  0
-  3  4  2  0  0  0  0
-  3  5  1  0  0  0  0
-  5  6  2  0  0  0  0
-  6  7  1  0  0  0  0
-  6 11  1  0  0  0  0
-  7  8  1  0  0  0  0
-  9  8  1  6  0  0  0
- 10  9  1  1  0  0  0
-
------
-
-.. class:: infomark
-
-**Cite**
-
-Confab_
-
-.. _Confab: https://code.google.com/p/confab/
-
-
-]]>
-    </help>
-</tool>
diff -r 731ad135ddb4 -r 548537fc2577 osra.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/osra.py	Sun Nov 01 10:31:42 2015 -0500
@@ -0,0 +1,27 @@
+#!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[7]):
+    # 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
+
+sys.argv[0] = 'osra'
+subprocess.call(sys.argv, stdout=sys.stdout)
+
+
diff -r 731ad135ddb4 -r 548537fc2577 osra.tar.bz2
Binary file osra.tar.bz2 has changed
diff -r 731ad135ddb4 -r 548537fc2577 osra.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/osra.xml	Sun Nov 01 10:31:42 2015 -0500
@@ -0,0 +1,78 @@
+<tool id="ctb_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>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+        <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+    </requirements>
+    <command interpreter='python'>
+<![CDATA[
+        ## 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
+
+        $confidence
+        $adaptive
+        $thinning
+
+        > $outfile
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
+        <param name="oformat" type="select" label="Output molecule format">
+            <option value="can">SMILES</option>
+            <option value="sdf">SDF</option>
+        </param>
+        <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" />
+        <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" />
+        <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" type="data" format="sdf">
+            <change_format>
+                <when input="oformat" value="can" format="smi"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="png" value="CID_2244.png"/>
+            <param name="oformat" value="sdf"/>
+            <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
+        </test>
+        <test>
+            <param name="infile" ftype="png" value="2008001635_153_chem.png"/>
+            <param name="oformat" value="can"/>
+            <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/>
+        </test>
+
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+OSRA_ (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures into SMILES or SDF. It generates the SMILES or SDF representation of any molecular structure image within a document which is parseable by GraphicMagick.
+
+.. _OSRA: http://cactus.nci.nih.gov/osra/
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_
+
+.. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r
+]]>
+    </help>
+</tool>
diff -r 731ad135ddb4 -r 548537fc2577 readme
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme	Sun Nov 01 10:31:42 2015 -0500
@@ -0,0 +1,20 @@
+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.
diff -r 731ad135ddb4 -r 548537fc2577 test-data/CID_3033.sdf
--- a/test-data/CID_3033.sdf	Sun Nov 01 10:28:54 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,271 +0,0 @@
-3033
-  -OEChem-08231107463D
-
- 30 31  0     0  0  0  0  0  0999 V2000
-    1.9541    1.1500   -2.5078 Cl  0  0  0  0  0  0  0  0  0  0  0  0
-    1.1377   -1.6392    2.1136 Cl  0  0  0  0  0  0  0  0  0  0  0  0
-   -3.2620   -2.9284   -1.0647 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.7906   -1.9108    0.9092 O   0  0  0  0  0  0  0  0  0  0  0  0
-    0.2679   -0.2051   -0.3990 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.0640    0.5139   -0.3769 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.7313    0.7178   -0.0192 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.4761   -0.6830   -1.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
-    1.6571   -0.2482   -0.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.0382    1.4350    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.3728    1.8429    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.6797    2.5600    0.7506 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.3470    2.7640    1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.5353    0.3477   -1.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.1740   -0.8865    0.9534 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.8480   -1.8749   -0.3123 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.9124    0.3058   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.5511   -0.9285    1.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
-    4.4203   -0.3324    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.7086   -0.9792   -1.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.3614   -0.4266   -1.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.0861   -1.1146   -0.6780 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -4.0812    1.2885   -0.2604 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.6569    2.0278    1.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.4382    3.2769    1.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.0683    3.6399    1.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
-    4.6037    0.7654   -1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
-    3.9635   -1.4215    2.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4925   -0.3651    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.5025   -3.7011   -0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
-  1 14  1  0  0  0  0
-  2 15  1  0  0  0  0
-  3 16  1  0  0  0  0
-  3 30  1  0  0  0  0
-  4 16  2  0  0  0  0
-  5  7  1  0  0  0  0
-  5  9  1  0  0  0  0
-  5 22  1  0  0  0  0
-  6  7  1  0  0  0  0
-  6  8  1  0  0  0  0
-  6 10  2  0  0  0  0
-  7 11  2  0  0  0  0
-  8 16  1  0  0  0  0
-  8 20  1  0  0  0  0
-  8 21  1  0  0  0  0
-  9 14  2  0  0  0  0
-  9 15  1  0  0  0  0
- 10 12  1  0  0  0  0
- 10 23  1  0  0  0  0
- 11 13  1  0  0  0  0
- 11 24  1  0  0  0  0
- 12 13  2  0  0  0  0
- 12 25  1  0  0  0  0
- 13 26  1  0  0  0  0
- 14 17  1  0  0  0  0
- 15 18  2  0  0  0  0
- 17 19  2  0  0  0  0
- 17 27  1  0  0  0  0
- 18 19  1  0  0  0  0
- 18 28  1  0  0  0  0
- 19 29  1  0  0  0  0
-M  END
-> <PUBCHEM_COMPOUND_CID>
-3033
-
-> <PUBCHEM_CONFORMER_RMSD>
-0.6
-
-> <PUBCHEM_CONFORMER_DIVERSEORDER>
-1
-20
-18
-39
-29
-42
-38
-35
-30
-25
-33
-28
-32
-36
-26
-24
-40
-11
-27
-37
-7
-41
-10
-19
-43
-8
-6
-16
-44
-23
-34
-14
-15
-31
-9
-13
-17
-21
-22
-5
-12
-2
-3
-4
-
-> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
-28
-1 -0.18
-10 -0.15
-11 -0.15
-12 -0.15
-13 -0.15
-14 0.18
-15 0.18
-16 0.66
-17 -0.15
-18 -0.15
-19 -0.15
-2 -0.18
-22 0.4
-23 0.15
-24 0.15
-25 0.15
-26 0.15
-27 0.15
-28 0.15
-29 0.15
-3 -0.65
-30 0.5
-4 -0.57
-5 -0.6
-6 -0.14
-7 0.1
-8 0.2
-9 0.1
-
-> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
-4
-
-> <PUBCHEM_PHARMACOPHORE_FEATURES>
-7
-1 3 acceptor
-1 4 acceptor
-1 5 cation
-1 5 donor
-3 3 4 16 anion
-6 6 7 10 11 12 13 rings
-6 9 14 15 17 18 19 rings
-
-> <PUBCHEM_HEAVY_ATOM_COUNT>
-19
-
-> <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_CONFORMER_ID>
-00000BD900000001
-
-> <PUBCHEM_MMFF94_ENERGY>
-65.6362
-
-> <PUBCHEM_FEATURE_SELFOVERLAP>
-35.578
-
-> <PUBCHEM_SHAPE_FINGERPRINT>
-10366900 7 17386020514759110480
-114674 6 16903282898360328323
-11578080 2 17913245089295617604
-11582403 64 14544541357940910356
-11640471 11 18127963303313961600
-12236239 1 18272088352834916308
-12363563 72 18042978579496277287
-12553582 1 18190740839094073615
-12596599 1 18201439237582433270
-12788726 201 18410285909464206003
-13032168 30 18201440238019390274
-13140716 1 18187086113919468457
-13538477 17 18339642338307470464
-13583140 156 17241914119188522922
-13764800 53 17895191172601517065
-13965767 371 17259888045752176376
-14115302 16 18342181093776810149
-14787075 74 17907866106787333628
-15279307 12 18198622322777022915
-15375462 189 18270674264943931347
-15669948 3 18336550511731321249
-16752209 62 18336841852664817743
-16945 1 18188484791351783177
-19433438 48 18059583550169763352
-200 152 18130792217719576158
-20645476 183 18270115859187436189
-20905425 154 17970632883131290416
-21452121 199 18046637711133085653
-21639500 275 16988270998321974524
-22112679 90 18342446063036096292
-23419403 2 17835564502519425292
-23493267 7 18115023138028600728
-23526113 38 16660924516543134566
-23557571 272 17821721762863303772
-23559900 14 17896315990920094510
-23598288 3 18411412925846384519
-23598291 2 18059009613384180254
-238 59 16343141308025475526
-4340502 62 17273677940604857177
-6049 1 17240202131864233360
-6992083 37 18058168521433072460
-7615 1 18201433675414973908
-77492 1 18272651289913926852
-81228 2 17968373550240022809
-9709674 26 17896035610527288590
-
-> <PUBCHEM_SHAPE_MULTIPOLES>
-378.03
-7.01
-2.75
-1.77
-0.78
-1.58
-0.3
-0.41
-1.94
--1.08
-1.9
--8.69
-11.04
-2.58
-
-> <PUBCHEM_SHAPE_SELFOVERLAP>
-790.335
-
-> <PUBCHEM_SHAPE_VOLUME>
-214.7
-
-> <PUBCHEM_COORDINATE_TYPE>
-2
-5
-255
-
-$$$$
-
diff -r 731ad135ddb4 -r 548537fc2577 test-data/confab_on_CID3033.sdf
--- a/test-data/confab_on_CID3033.sdf	Sun Nov 01 10:28:54 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,270 +0,0 @@
-214.7
- OpenBabel06291213403D
-
- 30 31  0  0  0  0  0  0  0  0999 V2000
-    1.9541    1.1500   -2.5078 Cl  0  0  0  0  0  0  0  0  0  0  0  0
-    1.1377   -1.6392    2.1136 Cl  0  0  0  0  0  0  0  0  0  0  0  0
-   -3.2620   -2.9284   -1.0647 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.7906   -1.9108    0.9092 O   0  0  0  0  0  0  0  0  0  0  0  0
-    0.2679   -0.2051   -0.3990 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.0640    0.5139   -0.3769 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.7313    0.7178   -0.0192 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.4761   -0.6830   -1.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
-    1.6571   -0.2482   -0.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.0382    1.4350    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.3728    1.8429    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.6797    2.5600    0.7506 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.3470    2.7640    1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.5353    0.3477   -1.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.1740   -0.8865    0.9534 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.8480   -1.8749   -0.3123 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.9124    0.3058   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.5511   -0.9285    1.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
-    4.4203   -0.3324    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.7086   -0.9792   -1.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.3614   -0.4266   -1.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.0861   -1.1146   -0.6780 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -4.0812    1.2885   -0.2604 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.6569    2.0278    1.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.4382    3.2769    1.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.0683    3.6399    1.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
-    4.6037    0.7654   -1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
-    3.9635   -1.4215    2.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4925   -0.3651    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.5025   -3.7011   -0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
-  1 14  1  0  0  0  0
-  2 15  1  0  0  0  0
-  3 16  1  0  0  0  0
-  3 30  1  0  0  0  0
-  4 16  2  0  0  0  0
-  5  7  1  0  0  0  0
-  5  9  1  0  0  0  0
-  5 22  1  0  0  0  0
-  6  7  1  0  0  0  0
-  6  8  1  0  0  0  0
-  6 10  2  0  0  0  0
-  7 11  2  0  0  0  0
-  8 16  1  0  0  0  0
-  8 20  1  0  0  0  0
-  8 21  1  0  0  0  0
-  9 14  2  0  0  0  0
-  9 15  1  0  0  0  0
- 10 12  1  0  0  0  0
- 10 23  1  0  0  0  0
- 11 13  1  0  0  0  0
- 11 24  1  0  0  0  0
- 12 13  2  0  0  0  0
- 12 25  1  0  0  0  0
- 13 26  1  0  0  0  0
- 14 17  1  0  0  0  0
- 15 18  2  0  0  0  0
- 17 19  2  0  0  0  0
- 17 27  1  0  0  0  0
- 18 19  1  0  0  0  0
- 18 28  1  0  0  0  0
- 19 29  1  0  0  0  0
-M  END
->  <PUBCHEM_COMPOUND_CID>
-3033
-
->  <PUBCHEM_CONFORMER_RMSD>
-0.6
-
->  <PUBCHEM_CONFORMER_DIVERSEORDER>
-1
-20
-18
-39
-29
-42
-38
-35
-30
-25
-33
-28
-32
-36
-26
-24
-40
-11
-27
-37
-7
-41
-10
-19
-43
-8
-6
-16
-44
-23
-34
-14
-15
-31
-9
-13
-17
-21
-22
-5
-12
-2
-3
-4
-
->  <PUBCHEM_MMFF94_PARTIAL_CHARGES>
-28
-1 -0.18
-10 -0.15
-11 -0.15
-12 -0.15
-13 -0.15
-14 0.18
-15 0.18
-16 0.66
-17 -0.15
-18 -0.15
-19 -0.15
-2 -0.18
-22 0.4
-23 0.15
-24 0.15
-25 0.15
-26 0.15
-27 0.15
-28 0.15
-29 0.15
-3 -0.65
-30 0.5
-4 -0.57
-5 -0.6
-6 -0.14
-7 0.1
-8 0.2
-9 0.1
-
->  <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
-4
-
->  <PUBCHEM_PHARMACOPHORE_FEATURES>
-7
-1 3 acceptor
-1 4 acceptor
-1 5 cation
-1 5 donor
-3 3 4 16 anion
-6 6 7 10 11 12 13 rings
-6 9 14 15 17 18 19 rings
-
->  <PUBCHEM_HEAVY_ATOM_COUNT>
-19
-
->  <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_CONFORMER_ID>
-00000BD900000001
-
->  <PUBCHEM_MMFF94_ENERGY>
-65.6362
-
->  <PUBCHEM_FEATURE_SELFOVERLAP>
-35.578
-
->  <PUBCHEM_SHAPE_FINGERPRINT>
-10366900 7 17386020514759110480
-114674 6 16903282898360328323
-11578080 2 17913245089295617604
-11582403 64 14544541357940910356
-11640471 11 18127963303313961600
-12236239 1 18272088352834916308
-12363563 72 18042978579496277287
-12553582 1 18190740839094073615
-12596599 1 18201439237582433270
-12788726 201 18410285909464206003
-13032168 30 18201440238019390274
-13140716 1 18187086113919468457
-13538477 17 18339642338307470464
-13583140 156 17241914119188522922
-13764800 53 17895191172601517065
-13965767 371 17259888045752176376
-14115302 16 18342181093776810149
-14787075 74 17907866106787333628
-15279307 12 18198622322777022915
-15375462 189 18270674264943931347
-15669948 3 18336550511731321249
-16752209 62 18336841852664817743
-16945 1 18188484791351783177
-19433438 48 18059583550169763352
-200 152 18130792217719576158
-20645476 183 18270115859187436189
-20905425 154 17970632883131290416
-21452121 199 18046637711133085653
-21639500 275 16988270998321974524
-22112679 90 18342446063036096292
-23419403 2 17835564502519425292
-23493267 7 18115023138028600728
-23526113 38 16660924516543134566
-23557571 272 17821721762863303772
-23559900 14 17896315990920094510
-23598288 3 18411412925846384519
-23598291 2 18059009613384180254
-238 59 16343141308025475526
-4340502 62 17273677940604857177
-6049 1 17240202131864233360
-6992083 37 18058168521433072460
-7615 1 18201433675414973908
-77492 1 18272651289913926852
-81228 2 17968373550240022809
-9709674 26 17896035610527288590
-
->  <PUBCHEM_SHAPE_MULTIPOLES>
-378.03
-7.01
-2.75
-1.77
-0.78
-1.58
-0.3
-0.41
-1.94
--1.08
-1.9
--8.69
-11.04
-2.58
-
->  <PUBCHEM_SHAPE_SELFOVERLAP>
-790.335
-
->  <PUBCHEM_SHAPE_VOLUME>
-214.7
-
->  <PUBCHEM_COORDINATE_TYPE>
-2
-5
-255
-
-$$$$
diff -r 731ad135ddb4 -r 548537fc2577 test_data/2008001635_153_chem.png
Binary file test_data/2008001635_153_chem.png has changed
diff -r 731ad135ddb4 -r 548537fc2577 test_data/2008001635_153_chem.smi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/2008001635_153_chem.smi	Sun Nov 01 10:31:42 2015 -0500
@@ -0,0 +1,1 @@
+CCC(c1ccc(cc1)Br)OCCCO
diff -r 731ad135ddb4 -r 548537fc2577 test_data/CID_2244.png
Binary file test_data/CID_2244.png has changed
diff -r 731ad135ddb4 -r 548537fc2577 test_data/CID_2244.sdf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/CID_2244.sdf	Sun Nov 01 10:31:42 2015 -0500
@@ -0,0 +1,155 @@
+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
+
+$$$$
+
diff -r 731ad135ddb4 -r 548537fc2577 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Nov 01 10:28:54 2015 -0500
+++ b/tool_dependencies.xml	Sun Nov 01 10:31:42 2015 -0500
@@ -1,30 +1,74 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="eigen2" version="2.0.17">
-        <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="openbabel" version="2.3.2">
+        <repository changeset_revision="e5ef70185d24" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="confab" version="1.0.1">
+    <package name="graphicsmagick" version="1.3.18">
+        <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="osra" version="2.0.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://github.com/bgruening/confab/archive/1.0.1.tar.gz</action>
+                <!-- first action is always downloading -->
+                <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action>
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="eigen2" version="2.0.17" />
+                    <repository changeset_revision="e5ef70185d24" name="package_openbabel_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="openbabel" version="2.3.2" />
+                    </repository>
+                    <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="graphicsmagick" version="1.3.18" />
                     </repository>
                 </action>
 
-                <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR=$EIGEN2_SOURCE_PATH</action>
+                <!--compiling potrace-1.11 -->
+                <action type="download_file">http://potrace.sourceforge.net/download/1.11/potrace-1.11.tar.gz</action>
+                <action type="shell_command">tar xfvz potrace-1.11.tar.gz &amp;&amp; cd potrace-1.11 &amp;&amp; ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--compiling gocr 0.50patched -->
+                <!-- not yet possible
+                <action type="download_file">http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action>
+                <action type="shell_command">tar xfvz gocr-0.50.tar.gz &amp;&amp; cd gocr-0.50 &amp;&amp; ./configure -|-prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
+                -->
+                <action type="download_file">http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
+                <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
+
+
+                <!--compiling tclap 1.2.1 -->
+                <action type="download_file">http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action>
+                <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz &amp;&amp; cd tclap-1.2.1 &amp;&amp; ./configure --prefix=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--compiling ocrad 0.21 -->
+                <action type="download_file">http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action>
+                <action type="shell_command">tar xfvz ocrad-0.21.tar.gz &amp;&amp; cd ocrad-0.21 &amp;&amp; ./configure --prefix=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--compiling cuneiform 1.1.0 -->
+                <action type="download_file">https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action>
+                <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 &amp;&amp; cd cuneiform-linux-1.1.0 &amp;&amp; mkdir build &amp;&amp; cd build &amp;&amp; cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--And finally OSRA 1.4.0-->
+                <!-- Extending the PATH is needed for OSRA -->
+                <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ &amp;&amp;
+                    ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$GRAPHICSMAGICK_ROOT_DIR/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action>
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install</action>
+
+                <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action>
+                <!--<action type="shell_command">rm $INSTALL_DIR/openbabel/ -r</action>-->
+                <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action>
+                <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action>
+                <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action>
+
                 <action type="set_environment">
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="BABEL_DATADIR">$INSTALL_DIR/share/openbabel</environment_variable>
-                    <environment_variable action="set_to" name="BABEL_LIBDIR">$INSTALL_DIR/lib/openbabel/2.2.99</environment_variable>
+                    <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA -->
+                    <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>Compiling Confab requires g++, CMake 2.4+. Optional but required for a few features is libxml2 and zlib.</readme>
+        <readme>We still have a handfull of requirements</readme>
     </package>
 </tool_dependency>