view mayatoolV1.xml @ 7:1085e4f6d061 draft

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<tool id="mayatoolsbar45se11" name="mayatools" version="0.0.1">
    <description>extract data from file according to field name and Ids </description>
  <requirements>
         <requirement type="package" version="9.0">mayachemtools</requirement>
    
   
</requirements>
    <command interpreter=""> 
<![CDATA[ 
#if '.sdf' in $inputsdf.name
/bin/mkdir -p $inputsdf.extra_files_path;
ln -sf $inputsdf $inputsdf.extra_files_path/molecules.sdf;
ExtractFromSDFiles.pl -o -m datafieldbylist -d  $Identifier,`cat ${indexnumbers}`  -r $outputsdf.name $inputsdf.extra_files_path/molecules.sdf > $logs;
/bin/rm -rf $inputsdf.extra_files_path;
cp $outputsdf.name $outputsdf;
#end if
 ]]>
 </command>
    <inputs>
        <param name="inputsdf" type="data" format="sdf" label="Original SDF File " help="sdf file from which selected ids of molecules  need to be extracted." />
        <param name="Identifier" type="text" label="Field name" help="Give field name of molecules on which compound need to be extracted Ex. MolID,PUBCHEM_COMPOUND_ID,CID etc." />
        <param name="indexnumbers" type="data" format="txt" label="Id file which need to be extracted from dataset" help="select file of ids ie. result file obtained from the tool 'Extract IDs From Prediction Result'" />

        <!--param name="max_olap" type="integer" value="50" label="Set maximum overlap length" help="Overlaps this short or shorter are ignored." /-->
        </inputs>
    <outputs>
        <data name="outputsdf" type="txt" format="sdf" label="extracted_cpds_from_${inputsdf.name}.sdf" />
        <data name="logs" format="txt" label="logfile" />
                  
        </outputs>
    <tests>
        
    </tests>
  </tool>