Mercurial > repos > anmoljh > compound_id_extract
changeset 0:179e2578e4c0 draft default tip
planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
author | anmoljh |
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date | Mon, 12 Jun 2017 08:51:28 -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 Mon Jun 12 08:51:28 2017 -0400 @@ -0,0 +1,28 @@ +<?xml version="1.0"?> +<tool id="extract_compound_id" name="Extract Compound IDs From Prediction Result" version="1.0"> +<description>This tool extract the compound name/ids 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>