# HG changeset patch # User yating-l # Date 1482176977 18000 # Node ID cf258ca024ffaa334cf838cc982b8c0876bbdcf0 # Parent e9dcea52d07979be677c36253b46ffa2e8eaf2e7 planemo upload commit ca69686dfafcabb815c93fd46d3c4dfe57459e39-dirty diff -r e9dcea52d079 -r cf258ca024ff README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Dec 19 14:49:37 2016 -0500 @@ -0,0 +1,6 @@ +# regtools +A Galaxy Wrapper for regtools + +This is a modified Galaxy wrapper for regtools which is based on the previous wrapper written by Remi Marenco (https://github.com/remimarenco/regtools). "regtools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context" (https://regtools.readthedocs.io/en/latest/). + +This wrapper add an validation step to check if the output files are valid BED format. The lines with invalid strand (neighter "+" or "-") will be removed. The scores higher than 1000 will be changed to 1000. All modified lines will be reported to the standard output. diff -r e9dcea52d079 -r cf258ca024ff regtools_junctions_extract.xml --- a/regtools_junctions_extract.xml Mon Dec 19 13:21:56 2016 -0500 +++ b/regtools_junctions_extract.xml Mon Dec 19 14:49:37 2016 -0500 @@ -100,7 +100,7 @@ - + 1000): + scoreLines.append("line" + str(i) + ":" + line) + fields[4] = '1000' if (strand == '+' or strand == '-'): tmp.write('\t'.join(map(str, fields))) tmp.write("\n") @@ -25,15 +27,18 @@ removedLines.append("line" + str(i) + ": " + line) i = i+1 - return removedLines + return removedLines, scoreLines def main(): inputfile = str(sys.argv[1]) outputfile = str(sys.argv[2]) - removed = checkAndFixBed(inputfile, outputfile) + removed, changed = checkAndFixBed(inputfile, outputfile) if (removed != []): print "\nRemoved invalid lines: \n" print "\n".join(removed) + if (changed != []): + print "\nThe following lines have scores > 1000, so they are changed to 1000:\n" + print "\n".join(changed) if __name__ == "__main__": main()