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1 <tool id="mayatoolsbase11" name="mayatools" version="1.0.1">
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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="set_environment">MAYA_TOOL3_PATH</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 #if '.sdf' in $inputsdf.name
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10 /bin/mkdir $inputsdf.extra_files_path;
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11 ln -s $inputsdf $inputsdf.extra_files_path/molecules.sdf;
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12 /usr/bin/perl \$MAYA_TOOL3_PATH/test.pl $outputsdf.name $inputsdf.extra_files_path/molecules.sdf $Identifier $indexnumbers > $logs;
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13 /bin/rm -rf $inputsdf.extra_files_path;
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14 cp $outputsdf.name $outputsdf;
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15 #end if
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16 </command>
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17 <inputs>
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18 <param name="inputsdf" type="data" format="sdf" label="Original SDF File " help="sdf file from which selected ids of molecules need to be extracted." />
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19 <param name="Identifier" type="text" label="Field name" help="Give field name of molecules on which compound need to be extracted Ex. MolID,PUBCHEM_COMPOUND_ID,CID etc." />
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20 <param name="indexnumbers" type="data" format="txt" label="Id file which need to be extracted from dataset" help="select file of ids ie. result file obtained from the tool 'Extract IDs From Prediction Result'" />
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21
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22 <!--param name="max_olap" type="integer" value="50" label="Set maximum overlap length" help="Overlaps this short or shorter are ignored." /-->
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23 </inputs>
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24 <outputs>
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25 <data name="outputsdf" type="txt" format="sdf" label="extracted_cpds_from_${inputsdf.name}.sdf" />
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26 <data name="logs" format="txt" label="logfile" />
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27
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28 </outputs>
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29 <tests>
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30
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31 </tests>
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32 </tool>
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