changeset 7:1085e4f6d061 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayatoolV1.xml	Thu Dec 15 14:05:50 2016 -0500
@@ -0,0 +1,34 @@
+<tool id="mayatoolsbar45se11" name="mayatools" version="0.0.1">
+    <description>extract data from file according to field name and Ids </description>
+  <requirements>
+         <requirement type="package" version="9.0">mayachemtools</requirement>
+    
+   
+</requirements>
+    <command interpreter=""> 
+<![CDATA[ 
+#if '.sdf' in $inputsdf.name
+/bin/mkdir -p $inputsdf.extra_files_path;
+ln -sf $inputsdf $inputsdf.extra_files_path/molecules.sdf;
+ExtractFromSDFiles.pl -o -m datafieldbylist -d  $Identifier,`cat ${indexnumbers}`  -r $outputsdf.name $inputsdf.extra_files_path/molecules.sdf > $logs;
+/bin/rm -rf $inputsdf.extra_files_path;
+cp $outputsdf.name $outputsdf;
+#end if
+ ]]>
+ </command>
+    <inputs>
+        <param name="inputsdf" type="data" format="sdf" label="Original SDF File " help="sdf file from which selected ids of molecules  need to be extracted." />
+        <param name="Identifier" type="text" label="Field name" help="Give field name of molecules on which compound need to be extracted Ex. MolID,PUBCHEM_COMPOUND_ID,CID etc." />
+        <param name="indexnumbers" type="data" format="txt" label="Id file which need to be extracted from dataset" help="select file of ids ie. result file obtained from the tool 'Extract IDs From Prediction Result'" />
+
+        <!--param name="max_olap" type="integer" value="50" label="Set maximum overlap length" help="Overlaps this short or shorter are ignored." /-->
+        </inputs>
+    <outputs>
+        <data name="outputsdf" type="txt" format="sdf" label="extracted_cpds_from_${inputsdf.name}.sdf" />
+        <data name="logs" format="txt" label="logfile" />
+                  
+        </outputs>
+    <tests>
+        
+    </tests>
+  </tool>