<tool id="ExtractFromSDFiles" name="ExtractFromSDFiles" version="1.0">
<description>extracts data from file according to field Name and IDs</description>
<requirements>
     <requirement type="package" version="9.0">mayachemtools</requirement>
</requirements>
<stdio>
     <exit_code range="1:" />
</stdio>

<command> <![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'" />
    </inputs>
    <outputs>
        <data name="outputsdf" format="sdf" label="extracted_cpds_from_${inputsdf.name}" />
        <data name="logs" format="txt" label="logfile" />
    </outputs>
    <tests>
        <test>
              <param name="inputsdf" value="Pred_set.sdf"  />
	      <param name="Identifier" value="MOLECULE_NAME" />
	      <param name="indexnumbers" value="extracted_ids.txt"  />
	      <output name="outputsdf" file="extracted_cpds.sdf" compare="sim_size" delta="8000000" />
	      <output name="logs" file="ext_log.txt" compare="sim_size" delta="800000" />
        </test>
    </tests>
</tool>