Mercurial > repos > galaxyp > gffcompare_to_bed
changeset 2:9a4cfc910674 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
| author | galaxyp |
|---|---|
| date | Tue, 07 Apr 2020 11:36:42 -0400 |
| parents | 0f62097d7c1a |
| children | ba5368c19dbd |
| files | gffcompare_to_bed.py gffcompare_to_bed.xml |
| diffstat | 2 files changed, 9 insertions(+), 7 deletions(-) [+] |
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--- a/gffcompare_to_bed.py Fri Apr 26 14:42:31 2019 -0400 +++ b/gffcompare_to_bed.py Tue Apr 07 11:36:42 2020 -0400 @@ -31,13 +31,13 @@ self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100' self.blockCount = int(blockCount) - if isinstance(blockSizes, str) or isinstance(blockSizes, unicode): + if isinstance(blockSizes, str): self.blockSizes = [int(x) for x in blockSizes.split(',')] elif isinstance(blockSizes, list): self.blockSizes = [int(x) for x in blockSizes] else: self.blockSizes = blockSizes - if isinstance(blockStarts, str) or isinstance(blockSizes, unicode): + if isinstance(blockStarts, str): self.blockStarts = [int(x) for x in blockStarts.split(',')] elif isinstance(blockStarts, list): self.blockStarts = [int(x) for x in blockStarts] @@ -93,10 +93,9 @@ for j in attributes.rstrip(';').split(';')]} if feature == 'transcript': if args.debug: - print >> sys.stderr, "%s\t%s"\ - % ('\t'.join([seqname, source, feature, - start, end, score, strand, frame]), - attribute) + sys.stderr.write("%s\t%s\n" % ('\t'.join([seqname, source, + feature, start, end, score, strand, frame]), + attribute)) if bed is not None: write_bed_entry(bed) bed = None
--- a/gffcompare_to_bed.xml Fri Apr 26 14:42:31 2019 -0400 +++ b/gffcompare_to_bed.xml Tue Apr 07 11:36:42 2020 -0400 @@ -1,5 +1,8 @@ -<tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.2.0"> +<tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.2.1"> <description>for StringTie results</description> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/gffcompare_to_bed.py' #if $class_codes: