# HG changeset patch
# User deepakjadmin
# Date 1452090996 18000
# Node ID 28319c6588ffae566c44e0b9d3eb71afd9c233fd
# Parent 5de5c4d3c7401ef2ebecdda8b80afb369ba34126
Uploaded
diff -r 5de5c4d3c740 -r 28319c6588ff addact.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/addact.xml Wed Jan 06 09:36:36 2016 -0500
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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 5de5c4d3c740 -r 28319c6588ff padelnew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/padelnew.xml Wed Jan 06 09:36:36 2016 -0500
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+ 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 $PACKAGE_BASE/bin/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 $PACKAGE_BASE/bin/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 5de5c4d3c740 -r 28319c6588ff removeduplecate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/removeduplecate.xml Wed Jan 06 09:36:36 2016 -0500
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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 5de5c4d3c740 -r 28319c6588ff tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Jan 06 09:36:36 2016 -0500
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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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