annotate PaDEL-descriptor.xml @ 2:d35153edd310 draft default tip

planemo upload commit 14622cfccfaec931b5937c5172d661de0ed69861-dirty

<tool id="padel_descriptor" name="PaDEL-descriptor" version="1.0">
<requirements>
     <requirement type="package" version="1.0">padeldescriptor</requirement>
</requirements>
<stdio>
        <exit_code range="1:" />
</stdio>

<description>calculates descriptors for active and inactive datasets</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>