changeset 2:dfff2614510e draft

Deleted selected files

--- a/mayatoolV1.xml	Wed Jan 20 12:02:58 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<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>

--- a/test.pl	Wed Jan 20 12:02:58 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-#!/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" );

--- a/tool_dependencies.xml	Wed Jan 20 12:02:58 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<?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>