ipcress_gff.xml

<?xml version="1.0"?>
<tool id="ipcress_gff" name="IPCRESS to GFF">
        <description>Convert output from In-Silico PCR Experiment Simulation System to GFF format</description>
        <command>
                awk '/^ipcress:/, split($2,HIT,":"){print HIT[1],$3,$4,$5,$6,$7,$8,$9,$10,$11}' $input1 | awk -v OFS='\t' '{print $1,"ipcress","PCR_product",$5,$8,".","+",".","Name="$2}' > $output1
        </command>
        <inputs>
                <param format="txt" name="input1" type="data" label="iPCRESS ouptut" />
        </inputs>
        <outputs>
                <data format="gff" name="output1" />
        </outputs>
        <tests>
        <test>
                <param name="input1" value="ipcress.out" ftype="txt" />
                <output name="output1" file="ipcress_gff.out" />
        </test>
        </tests>
        <help>
Uses awk to parse IPCRESS output to gff file format
        </help>
</tool>