diff osra.xml @ 2:548537fc2577 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty

--- /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>