Mercurial > repos > deepakjadmin > padel_descriptors_test1

changeset 14:9fcaec441269 draft

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Deleted selected files
author deepakjadmin
date Thu, 07 Jan 2016 00:54:49 -0500
parents 424d0a0d545d
children ed12998b2014
files addact.xml padelnew.xml removeduplecate.xml tool_dependencies.xml
diffstat 4 files changed, 0 insertions(+), 150 deletions(-) [+]
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--- a/addact.xml	Thu Jan 07 00:25:04 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-<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>
--- a/padelnew.xml	Thu Jan 07 00:25:04 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<tool id="PaDEL789xsf1" name="PaDEL">
-<requirements>
-       <requirement type="set_environment">PADEL_PATH</requirement>
-    <requirement type="package" version="2.21">padel</requirement>
-   
-</requirements>
-
-
-<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_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
-</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>
--- a/removeduplecate.xml	Thu Jan 07 00:25:04 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-<tool id="aaapadel003" name="Remove redundancy">
-<description>"Removes Repeated Entry From File"</description>
-<command interpreter="Rscript">tool3/removeduplecate.R $Input1 $Non_redudant_mega_file</command>
-<inputs>
-<param format="txt" name="Input1" type="data" label="Merged Descriptor File" help="csv format"/>
-</inputs>
-<outputs>
-<data format="csv" name="Non_redudant_mega_file" label="Non-redundant Mega Descriptor File"/> 
-</outputs>
-<help>
-run command with Descriptor file and in csv format only .output file will be in CSV format.
-</help>
-</tool>
--- a/tool_dependencies.xml	Thu Jan 07 00:25:04 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-
-<set_environment version="1.0">
-        <environment_variable name="PADEL_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
-        </set_environment>
-    <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>