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annotate ExtractFromSDFiles.xml @ 0:e3086f60b0e4 draft

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author anmoljh
date Fri, 01 Jun 2018 04:57:02 -0400
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1 <tool id="ExtractFromSDFiles" name="ExtractFromSDFiles" version="1.0">
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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 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9
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10 <command> <![CDATA[
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11
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12 #if '.sdf' in $inputsdf.name
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13
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14 /bin/mkdir -p $inputsdf.extra_files_path;
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15 ln -sf $inputsdf $inputsdf.extra_files_path/molecules.sdf;
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16
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17 ExtractFromSDFiles.pl -o -m datafieldbylist -d $Identifier,`cat ${indexnumbers}` -r $outputsdf.name $inputsdf.extra_files_path/molecules.sdf > $logs;
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18
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19 /bin/rm -rf $inputsdf.extra_files_path;
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20 cp $outputsdf.name $outputsdf;
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21
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22 #end if
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23
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24 ]]> </command>
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25 <inputs>
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26 <param name="inputsdf" type="data" format="sdf" label="Original SDF File " help="sdf file from which selected ids of molecules need to be extracted." />
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27 <param name="Identifier" type="text" label="Field name" help="Give field name of molecules on which compound need to be extracted Ex. MolID,PUBCHEM_COMPOUND_ID,CID etc." />
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28 <param name="indexnumbers" type="data" format="txt" label="Id file which need to be extracted from dataset" help="select file of ids ie. result file obtained from the tool 'Extract IDs From Prediction Result'" />
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29 </inputs>
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30 <outputs>
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31 <data name="outputsdf" format="sdf" label="extracted_cpds_from_${inputsdf.name}" />
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32 <data name="logs" format="txt" label="logfile" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="inputsdf" value="Pred_set.sdf" />
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37 <param name="Identifier" value="MOLECULE_NAME" />
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38 <param name="indexnumbers" value="extracted_ids.txt" />
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39 <output name="outputsdf" file="extracted_cpds.sdf" compare="sim_size" delta="8000000" />
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40 <output name="logs" file="ext_log.txt" compare="sim_size" delta="800000" />
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41 </test>
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42 </tests>
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43 </tool>