Mercurial > repos > deepakjadmin > padel_descriptors_test1
changeset 4:1b8c54b9de55 draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 06 Jan 2016 09:14:21 -0500 |
| parents | 64c804de0681 |
| children | 8dd76b4e7470 |
| files | addact.xml padelnew.xml removeduplecate.xml tool2/addact.pl tool2/addact.pl.copy tool3/removeduplecate.R tool_dependencies.xml |
| diffstat | 7 files changed, 200 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/addact.xml Wed Jan 06 09:14:21 2016 -0500 @@ -0,0 +1,29 @@ +<tool id="aaapadel002" name="Merge files"> +<description>"Merge data files of Active and Inactive compounds "</description> +<command interpreter="perl">tool2/addact.pl $Input1 $Activity1 $Input2 $Activity2 $Merged_file</command> +<inputs> +<param format="csv" name="Input1" type="data" label="Descriptor File 1" help="Upload Active/Inactive descriptor file in csv format"/> + <!--param name="Activity1" type="select" label="Choose Appropriate Lable"> + <option value = "Active" selected="TRUE">Active</option> + <option value = "Inactive" >Inactive</option> + </param--> + <param name="Activity1" type="text" value="Active" label="Select type of molecules" help="write something which defines data eg active,positive,inactive,negative,etc." > + <validator type="empty_field" message="This field can't be left blank"/> + </param> + + <param format="txt" name="Input2" type="data" label="Descriptor File 2" help="Upload Active/Inactive descriptor file in csv format"/> + <param name="Activity2" type="text" value="Inactive" label="Select type of molecules" help="write something which defines data eg active,positive,inactive,negative,etc."> + <validator type="empty_field" message="This field can't be left blank"/> + </param> + <!--param name="Activity2" type="select" label="Choose appropriate Label"> + <option value = "Inactive" selected= "TRUE">Inactive</option> + <option value = "Active" >Active</option> + </param--> +</inputs> +<outputs> +<data format="csv" name="Merged_file" label="Merged Mega Descriptor File "/> +</outputs> +<help> +Provide descriptor files of active/positive and inactive/negative molecules and assign them properly. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/padelnew.xml Wed Jan 06 09:14:21 2016 -0500 @@ -0,0 +1,76 @@ +<tool id="PaDEL789xsf1" name="PaDEL"> +<description>"PaDEL Descriptor Calculation Tool"</description> +<command interpreter=""> +#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-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-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log >$log +#end if +</command> + +<inputs> + <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/> + + <param name="detectaromaticity" type="select" label="Detect the aroamaticity"> + <option value = "-detectaromaticity" selected="TRUE" >YES</option> + <option value = "" >NO</option> + </param> + + <param name="removesalt" type="select" label="Remove salt"> + <option value = "-removesalt" selected="TRUE" >YES</option> + <option value = "" >NO</option> + </param> + + <param name="standardizenitro" type="select" label="Standardize nitro groups"> + <option value = "-standardizenitro" selected="TRUE" >YES</option> + <option value = "" >NO</option> + </param> + + <param name="convert3d" type="select" label="convert in 3D"> + <option value = "" selected="TRUE" >NO</option> + <option value = "-convert3d" >YES</option> + </param> + + <param name="retain3d" type="select" label="Retain 3D coordinates"> + <option value = "" selected="TRUE" >NO</option> + <option value = "-retain3d" >YES</option> + + </param> + + <param name="coordinate" type="select" label="calculate 3d descriptors"> + <option value = "" selected="TRUE" >NO</option> + <option value = "-3d" >YES</option> + </param> + + <param name="fingerprint" type="select" label="calculate fingerprints"> + <option value = "" selected="TRUE" >NO</option> + <option value = "-fingerprints">YES</option> + </param> + + + <param name="retainorder" type="select" label="Retain molecules order"> + <option value = "-retainorder" selected="TRUE">YES</option> + <option value = "" >NO</option> + </param> + + + + <!-- +<param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" /> +<param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" /> +--> + </inputs> + +<outputs> + <data format="csv" name="descriptor" label="Descriptors File of $input.name "/> + <data format="txt" name="log" label="Log File of $input.name"/> +</outputs> + +<help> +Input may be any sdf,smile or mol2 file and output file will be in CSV format. +</help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/removeduplecate.xml Wed Jan 06 09:14:21 2016 -0500 @@ -0,0 +1,13 @@ +<tool id="aaapadel003" name="Remove redundancy"> +<description>"Removes Repeated Entry From File"</description> +<command interpreter="Rscript">tool3/removeduplecate.R $Input1 $Non_redudant_mega_file</command> +<inputs> +<param format="txt" name="Input1" type="data" label="Merged Descriptor File" help="csv format"/> +</inputs> +<outputs> +<data format="csv" name="Non_redudant_mega_file" label="Non-redundant Mega Descriptor File"/> +</outputs> +<help> +run command with Descriptor file and in csv format only .output file will be in CSV format. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool2/addact.pl Wed Jan 06 09:14:21 2016 -0500 @@ -0,0 +1,25 @@ +#!/usr/bin/perl +use warnings; +use strict; +open(FH,$ARGV[0]) or die "Couldn't open file, $!"; +open(DH,">$ARGV[4]") or die "Couldn't open file, $!"; +my $first_line = scalar <FH>; +chomp($first_line); +$first_line = join(",",$first_line,"outcome\n"); +print DH $first_line; +while(<FH>){chomp($_); +my $line= join(",",$_,"$ARGV[1]\n"); +print DH $line; +} +close FH; +open(SH,$ARGV[2]) or die "Coudn't open file,$!"; +scalar <SH>; +while(<SH>){ +if($ARGV[1] ne $ARGV[3]){chomp($_); +my $line1= join(",",$_,"$ARGV[3]\n"); +print DH $line1; +} +else{ print ("There is error to assign activity\n");exit;} +} +close SH; +close DH;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool2/addact.pl.copy Wed Jan 06 09:14:21 2016 -0500 @@ -0,0 +1,25 @@ +#!/usr/bin/perl +use warnings; +use strict; +open(FH,$ARGV[0]) or die "Couldn't open file, $!"; +open(DH,">tmp.txt") or die "Couldn't open file, $!"; +my $first_line = scalar <FH>; +chomp($first_line); +$first_line = join(",",$first_line,"outcome\n"); +print DH $first_line; +while(<FH>){chomp($_); +my $line= join(",",$_,"$ARGV[1]\n"); +print DH $line; +} +close FH; +open(SH,$ARGV[2]) or die "Coudn't open file,$!"; +scalar <SH>; +while(<SH>){ +if($ARGV[1] ne $ARGV[3]){chomp($_); +my $line1= join(",",$_,"$ARGV[3]\n"); +print DH $line1; +} +else{ print ("There is error to assign activity\n");exit;} +} +close SH; +close DH;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool3/removeduplecate.R Wed Jan 06 09:14:21 2016 -0500 @@ -0,0 +1,11 @@ +args <- commandArgs(TRUE) + + +res1 <- read.csv(args[1]) +#res11 <- duplicated(res1[,1:length(res1) - 1]) +res11 <- duplicated(res1[,1]) +result <- res1[!res11,] +names1 <- result[,1] +rownames(result) <- names1 +result$Name <- NULL +write.csv(result,file=args[2])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jan 06 09:14:21 2016 -0500 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="padel" version="2.21"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url">http://www.yapcwsoft.com/dd/padeldescriptor/PaDEL-Descriptor.zip</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin/</destination_directory> + </action> + </actions> + + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions_group> + </install> + <readme></readme> + </package> +</tool_dependency>