annotate extract_compound_id.xml @ 0:a45e6db3fdf0 draft default tip

planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272-dirty

<?xml version="1.0"?>
<tool id="extract_compound_id" name="Compound-ID Extractor" version="1.0">
<description>This tool extracts compound name/id from prediction result</description>
<stdio>
	<exit_code range="1:" />
</stdio>

<command><![CDATA[ 

awk -F '\t' '{print $1}' $predictionfile | sed '1d' | sed 's/"//g' | sed -e 's/^[ \t]*//;s/[ \t]*$//' | paste -sd "," - > $extracted_IDs ;

]]></command>

<inputs>
	<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'" /> 
</inputs>

<outputs>
	<data name="extracted_IDs" format="txt" label="Ids-${predictionfile.name}" />
</outputs>
<tests>
        <test>
        	<param name="predictionfile" value="selected_compounds.txt"  />
         	<output name="extracted_IDs" file="extracted_ids.txt" compare="sim_size" delta="2000" />
	</test>
</tests>
<help></help>
</tool>