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7
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1 <tool id="mayatoolsbar45se11" name="mayatools" version="0.0.1">
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2 <description>extract data from file according to field name and Ids </description>
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3 <requirements>
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4 <requirement type="package" version="9.0">mayachemtools</requirement>
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5
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6
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7 </requirements>
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8 <command interpreter="">
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9 <![CDATA[
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10 #if '.sdf' in $inputsdf.name
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11 /bin/mkdir -p $inputsdf.extra_files_path;
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12 ln -sf $inputsdf $inputsdf.extra_files_path/molecules.sdf;
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13 ExtractFromSDFiles.pl -o -m datafieldbylist -d $Identifier,`cat ${indexnumbers}` -r $outputsdf.name $inputsdf.extra_files_path/molecules.sdf > $logs;
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14 /bin/rm -rf $inputsdf.extra_files_path;
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15 cp $outputsdf.name $outputsdf;
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16 #end if
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="inputsdf" type="data" format="sdf" label="Original SDF File " help="sdf file from which selected ids of molecules need to be extracted." />
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21 <param name="Identifier" type="text" label="Field name" help="Give field name of molecules on which compound need to be extracted Ex. MolID,PUBCHEM_COMPOUND_ID,CID etc." />
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22 <param name="indexnumbers" type="data" format="txt" label="Id file which need to be extracted from dataset" help="select file of ids ie. result file obtained from the tool 'Extract IDs From Prediction Result'" />
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23
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24 <!--param name="max_olap" type="integer" value="50" label="Set maximum overlap length" help="Overlaps this short or shorter are ignored." /-->
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25 </inputs>
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26 <outputs>
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27 <data name="outputsdf" type="txt" format="sdf" label="extracted_cpds_from_${inputsdf.name}.sdf" />
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28 <data name="logs" format="txt" label="logfile" />
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29
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30 </outputs>
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31 <tests>
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32
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33 </tests>
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34 </tool>
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