Mercurial > repos > deepakjadmin > padel_descriptors_test1
changeset 10:1ed1be5611bb draft
Deleted selected files
| author | deepakjadmin |
|---|---|
| date | Wed, 06 Jan 2016 09:44:09 -0500 |
| parents | 28319c6588ff |
| children | c1ebd651da65 |
| files | padelnew.xml |
| diffstat | 1 files changed, 0 insertions(+), 83 deletions(-) [+] |
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--- a/padelnew.xml Wed Jan 06 09:36:36 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -<tool id="PaDEL789xsf1" name="PaDEL"> -<requirements> - - <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 $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 -</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>