diff osra.xml @ 11:143a63ca2bca

Uploaded

--- a/osra.xml	Thu May 23 02:57:31 2013 -0400
+++ b/osra.xml	Thu May 23 16:19:16 2013 -0400
@@ -1,7 +1,7 @@
-<tool id="osra" name="Molecule recognition" version="0.2">
+<tool id="osra" name="Molecule recognition" version="0.3">
     <description>in Images or PDF documents (OSRA)</description>
     <requirements>
-        <requirement type="package" version="1.4.0">osra</requirement>
+        <requirement type="package" version="2.0.0">osra</requirement>
     </requirements>
     <command interpreter='python'>
         ## OSRA_DATA_FILES is set during the toolshed Installation
@@ -12,6 +12,10 @@
         ## 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>
@@ -20,6 +24,10 @@
             <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">
@@ -34,6 +42,12 @@
             <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>