diff osra.xml @ 3:f4c48bb81097

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/osra.xml	Thu May 23 03:07:17 2013 -0400
@@ -0,0 +1,46 @@
+<tool id="osra" name="Molecule recognition" version="0.2">
+    <description>in Images or PDF documents (OSRA)</description>
+    <requirements>
+        <requirement type="package" version="1.4.0">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
+        
+        > $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>
+    </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>
+    </tests>
+    <help>
+
+**What it does**
+
+OSRA detects molecules in images and converts them to standard molecule formats. 
+
+
+    </help>
+</tool>