Mercurial > repos > anmoljh > compound_id_extract

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author anmoljh
date Fri, 01 Jun 2018 04:54:06 -0400
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1 <?xml version="1.0"?>
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2 <tool id="extract_compound_id" name="Compound-ID Extractor" version="1.0">
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3 <description>This tool extracts compound name/id from prediction result</description>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7
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8 <command><![CDATA[
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9
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10 awk -F '\t' '{print $1}' $predictionfile | sed '1d' | sed 's/"//g' | sed -e 's/^[ \t]*//;s/[ \t]*$//' | paste -sd "," - > $extracted_IDs ;
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11
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12 ]]></command>
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13
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14 <inputs>
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15 <param name="predictionfile" type="data" format="txt,csv,tabular" label="Predition Result File" help ="upload gcac prediction result file obtained from the tool 'Extract_Compound_IDs_From_Prediction_Result_based_on_scores'" />
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16 </inputs>
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17
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18 <outputs>
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19 <data name="extracted_IDs" format="txt" label="Ids-${predictionfile.name}" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="predictionfile" value="selected_compounds.txt" />
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24 <output name="extracted_IDs" file="extracted_ids.txt" compare="sim_size" delta="2000" />
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25 </test>
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26 </tests>
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27 <help></help>
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28 </tool>