Mercurial > repos > anmoljh > padel_descriptor_calculation
changeset 0:d43add074240 draft
planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
| author | anmoljh |
|---|---|
| date | Mon, 12 Jun 2017 07:58:32 -0400 |
| parents | |
| children | b00c48ea3e74 |
| files | PaDEL-descriptor.xml tool_dependencies.xml |
| diffstat | 2 files changed, 150 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PaDEL-descriptor.xml Mon Jun 12 07:58:32 2017 -0400 @@ -0,0 +1,144 @@ +<tool id="padel_descriptor" name="PaDEL-descriptor" version="1.0"> +<requirements> + <requirement type="set_environment">PADELPATH</requirement> +</requirements> +<stdio> + <exit_code range="1:" /> +</stdio> + +<description>"PaDEL Descriptor Calculation Tool"</description> + +<command><![CDATA[ + +#if '.smi' in $input.name + /bin/mkdir -p $input.extra_files_path; + ln -sf $input $input.extra_files_path/molecule.smi; + /usr/bin/java -jar \$PADELPATH/PaDEL-Descriptor.jar + -dir $input.extra_files_path/molecule.smi + $coordinate2d + -maxruntime $maxruntime + -waitingjobs $maxjob + -threads $thread + $detectaromaticity + $removesalt + $standardizenitro + $convert3d + $retain3d + $coordinate3d + $fingerprint + $retainorder + -file $descriptor -log > $log; + /bin/rm -rf $input.extra_files_path; +#else + /usr/bin/java -jar \$PADELPATH/PaDEL-Descriptor.jar + -dir $input + $coordinate2d + -maxruntime $maxruntime + -waitingjobs $maxjob + -threads $thread + $detectaromaticity + $removesalt + $standardizenitro + $convert3d + $retain3d + $coordinate3d + $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="maxruntime" type="integer" value="300000" label="Set run time for individual molecule" help="In miliseconds" > + <validator type="empty_field" message="This field can't be left blank"/> + </param> + + <param name="thread" type="integer" value="8" label="Workers for the job" help="Set number of threads. -1 for maximun " > + <validator type="empty_field" message="This field can't be left blank"/> + </param> + + <param name="maxjob" type="integer" value="-1" label="Maximum waiting job per thread. " help="Put -1 for maximum uitility or put positive inetger values upto 50" > + <validator type="empty_field" message="This field can't be left blank"/> + </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="coordinate2d" type="select" label="calculate 2d descriptors"> + <option value = "" >NO</option> + <option value = "-2d" selected="True" >YES</option> + </param> + + <param name="coordinate3d" 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 $input.name"/> + </outputs> + + <tests> + <test> + <param name="input" value="test.sdf" /> + <param name="detectaromaticity" value="-detectaromaticity" /> + <param name="removesalt" value="-removesalt" /> + <param name="standardizenitro" value="-standardizenitro" /> + <param name="convert3d" value="" /> + <param name="retain3d" value="-retain3d" /> + <param name="threads" value="8" /> + <param name="maxjob" value="8" /> + <param name="maxruntime" value="300000" /> + <param name="coordinate2d" value="-2d" /> + <param name="coordinate3d" value="-3d" /> + <param name="fingerprint" value="-fingerprints" /> + <param name="retainorder" value="-retainorder" /> + <output name="descriptor" file="descriptorfile.csv" compare="sim_size" delta="2000" /> + <output name="log" file="logs" compare="sim_size" delta="2000" /> + </test> + </tests> + + <help>Input may be any sdf,smile or mol2 file and output file will be in CSV format.</help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jun 12 07:58:32 2017 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="PADELPATH" action="set_to">$REPOSITORY_INSTALL_DIR/PaDEL</environment_variable> + </set_environment> +</tool_dependency>