Mercurial > repos > anmoljh > compound_id_extract
comparison extract_compound_id.xml @ 0:a45e6db3fdf0 draft default tip
planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272-dirty
author | anmoljh |
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date | Fri, 01 Jun 2018 04:54:06 -0400 |
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-1:000000000000 | 0:a45e6db3fdf0 |
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1 <?xml version="1.0"?> | |
2 <tool id="extract_compound_id" name="Compound-ID Extractor" version="1.0"> | |
3 <description>This tool extracts compound name/id from prediction result</description> | |
4 <stdio> | |
5 <exit_code range="1:" /> | |
6 </stdio> | |
7 | |
8 <command><![CDATA[ | |
9 | |
10 awk -F '\t' '{print $1}' $predictionfile | sed '1d' | sed 's/"//g' | sed -e 's/^[ \t]*//;s/[ \t]*$//' | paste -sd "," - > $extracted_IDs ; | |
11 | |
12 ]]></command> | |
13 | |
14 <inputs> | |
15 <param name="predictionfile" type="data" format="txt,csv,tabular" label="Predition Result File" help ="upload gcac prediction result file obtained from the tool 'Extract_Compound_IDs_From_Prediction_Result_based_on_scores'" /> | |
16 </inputs> | |
17 | |
18 <outputs> | |
19 <data name="extracted_IDs" format="txt" label="Ids-${predictionfile.name}" /> | |
20 </outputs> | |
21 <tests> | |
22 <test> | |
23 <param name="predictionfile" value="selected_compounds.txt" /> | |
24 <output name="extracted_IDs" file="extracted_ids.txt" compare="sim_size" delta="2000" /> | |
25 </test> | |
26 </tests> | |
27 <help></help> | |
28 </tool> |