comparison extract_compound_id.xml @ 0:a45e6db3fdf0 draft default tip

planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272-dirty
author anmoljh
date Fri, 01 Jun 2018 04:54:06 -0400
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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>