# HG changeset patch
# User deepakjadmin
# Date 1452144304 18000
# Node ID 424d0a0d545dc348a352579f120a4859e6935fb9
# Parent 8cd5cc3d95493d106462dcdccf6fd049c86776b7
Uploaded
diff -r 8cd5cc3d9549 -r 424d0a0d545d addact.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/addact.xml Thu Jan 07 00:25:04 2016 -0500
@@ -0,0 +1,29 @@
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+"Merge data files of Active and Inactive compounds "
+tool2/addact.pl $Input1 $Activity1 $Input2 $Activity2 $Merged_file
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+Provide descriptor files of active/positive and inactive/negative molecules and assign them properly.
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diff -r 8cd5cc3d9549 -r 424d0a0d545d padelnew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/padelnew.xml Thu Jan 07 00:25:04 2016 -0500
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+ PADEL_PATH
+ padel
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+"PaDEL Descriptor Calculation Tool"
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+#if '.smi' in $input.name
+/bin/mkdir $input.extra_files_path;
+ln -s $input $input.extra_files_path/molecule.smi;
+/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log > $log ;
+/bin/rm -rf $input.extra_files_path;
+#else
+/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log >$log
+#end if
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+Input may be any sdf,smile or mol2 file and output file will be in CSV format.
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diff -r 8cd5cc3d9549 -r 424d0a0d545d removeduplecate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/removeduplecate.xml Thu Jan 07 00:25:04 2016 -0500
@@ -0,0 +1,13 @@
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+"Removes Repeated Entry From File"
+tool3/removeduplecate.R $Input1 $Non_redudant_mega_file
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+run command with Descriptor file and in csv format only .output file will be in CSV format.
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diff -r 8cd5cc3d9549 -r 424d0a0d545d tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Jan 07 00:25:04 2016 -0500
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+ $REPOSITORY_INSTALL_DIR
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+ http://www.yapcwsoft.com/dd/padeldescriptor/PaDEL-Descriptor.zip
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+ .
+ $INSTALL_DIR/bin/
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+ $INSTALL_DIR/bin
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