# HG changeset patch
# User deepakjadmin
# Date 1452169045 18000
# Node ID 825a7522f67681e50090f16d2292fe34330ab340
# Parent 35cec4878f6039bb545752951746a07d2ae28713
Uploaded
diff -r 35cec4878f60 -r 825a7522f676 addact.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/addact.xml Thu Jan 07 07:17:25 2016 -0500
@@ -0,0 +1,36 @@
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+"Merge data files of Active and Inactive compounds "
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+ PADEL_PATH
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+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 35cec4878f60 -r 825a7522f676 padelnew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/padelnew.xml Thu Jan 07 07:17:25 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 35cec4878f60 -r 825a7522f676 removeduplecate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/removeduplecate.xml Thu Jan 07 07:17:25 2016 -0500
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+"Removes Repeated Entry From File"
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+ PADEL_PATH
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+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 35cec4878f60 -r 825a7522f676 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Jan 07 07:17:25 2016 -0500
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+ https://github.com/Deep2106/R-3.1.3caret/raw/padel/DataMiningWORK/GCAC_ON_GOLD_STAND_DATA/TOOLSHED_WORK_FINAL/r_caret_final_test/PaDEL/PADEL-USED/trp/PADEL-USED.zip
+ .
+ $INSTALL_PATH
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+ $INSTALL_DIR
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+ PaDEL v 2.18 installed successfully.
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