changeset 3:e420415a1799 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayatoolV1.xml	Wed Jan 20 12:16:47 2016 -0500
@@ -0,0 +1,32 @@
+<tool id="mayatoolsbar45se11" name="mayatools" version="0.0.1">
+    <description>extract data from file according to field name and Ids </description>
+  <requirements>
+       <requirement type="set_environment">MAYA_TOOL3_PATH</requirement>
+    
+   
+</requirements>
+    <command interpreter=""> 
+#if '.sdf' in $inputsdf.name
+/bin/mkdir $inputsdf.extra_files_path;
+ln -s $inputsdf $inputsdf.extra_files_path/molecules.sdf;
+/usr/bin/perl \$MAYA_TOOL3_PATH/test.pl $outputsdf.name $inputsdf.extra_files_path/molecules.sdf $Identifier $indexnumbers > $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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test.pl	Wed Jan 20 12:16:47 2016 -0500
@@ -0,0 +1,14 @@
+#!/usr/bin/perl -w
+use warnings;
+$out1 = $ARGV[0];
+$in1 = $ARGV[1];
+$fieldname = $ARGV[2];
+$idfiles = $ARGV[3];
+
+open(FILE, $idfiles) or die "Can't read file 'filename' [$!]\n";  
+@document = <FILE>; 
+close (FILE);
+$strw = join(",",@document);
+$strw =~ tr/\r\n//d;
+$fieldValues = join(",",$fieldname,$strw);
+system("mayachemtools/bin/ExtractFromSDFiles.pl -m datafieldbylist -d $fieldValues -r $out1 -o $in1" );

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jan 20 12:16:47 2016 -0500
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tool_dependency>
+
+<set_environment version="1.0">
+        <environment_variable name="MAYA_TOOL3_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
+        </set_environment>
+   
+</tool_dependency>