Mercurial > repos > john-mccallum > pcr_markers
comparison ipcress_gff.xml @ 5:b321e0517be3 draft
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| author | ben-warren |
|---|---|
| date | Thu, 22 May 2014 20:30:19 -0400 |
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| 4:be070a68521e | 5:b321e0517be3 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="ipcress_gff" name="IPCRESS to GFF"> | |
| 3 <description>Convert output from In-Silico PCR Experiment Simulation System to GFF format</description> | |
| 4 <command> | |
| 5 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 | |
| 6 </command> | |
| 7 <inputs> | |
| 8 <param format="txt" name="input1" type="data" label="iPCRESS ouptut" /> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data format="gff" name="output1" /> | |
| 12 </outputs> | |
| 13 <tests> | |
| 14 <test> | |
| 15 <param name="input1" value="ipcress.out" ftype="txt" /> | |
| 16 <output name="output1" file="ipcress_gff.out" /> | |
| 17 </test> | |
| 18 </tests> | |
| 19 <help> | |
| 20 Uses awk to parse IPCRESS output to gff file format | |
| 21 </help> | |
| 22 </tool> |