Mercurial > repos > anmoljh > compound_id_extract
changeset 0:a45e6db3fdf0 draft default tip
planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272-dirty
| author | anmoljh |
|---|---|
| date | Fri, 01 Jun 2018 04:54:06 -0400 |
| parents | |
| children | |
| files | extract_compound_id.xml |
| diffstat | 1 files changed, 28 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_compound_id.xml Fri Jun 01 04:54:06 2018 -0400 @@ -0,0 +1,28 @@ +<?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>