| Previous changeset 3:7a910b2c72ff (2016-03-30) Next changeset 5:199989365def (2016-04-04) |
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Commit message:
Uploaded |
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modified:
chipsequtil/map_to_known_genes.py chipsequtil/map_to_known_genes.xml |
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added:
chipsequtil/._map_to_known_genes.py chipsequtil/._map_to_known_genes.xml |
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| diff -r 7a910b2c72ff -r 0eaa8225a09a chipsequtil/._map_to_known_genes.py |
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| Binary file chipsequtil/._map_to_known_genes.py has changed |
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| diff -r 7a910b2c72ff -r 0eaa8225a09a chipsequtil/._map_to_known_genes.xml |
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| Binary file chipsequtil/._map_to_known_genes.xml has changed |
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| diff -r 7a910b2c72ff -r 0eaa8225a09a chipsequtil/map_to_known_genes.py --- a/chipsequtil/map_to_known_genes.py Wed Mar 30 15:22:19 2016 -0400 +++ b/chipsequtil/map_to_known_genes.py Mon Apr 04 14:52:14 2016 -0400 |
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| @@ -60,16 +60,6 @@ gene_ref = parse_gene_ref(args[0]) xref_fn = args[1] peaks_fn = args[2] - if opts.peaks_fmt == 'auto' : - path,ext = os.path.splitext(peaks_fn) - if ext.lower() == '.xls' : - opts.peaks_fmt = 'MACS' - elif ext.lower() == '.bed' : - opts.peaks_fmt = 'BED' - elif ext.lower() == '.narrowpeak' : - opts.peaks_fmt = 'BED' - else : - parser.error('Could not guess peaks file format by extension (%s), aborting'%ext) if opts.peaks_fmt == 'MACS' : peaks_reader_cls = MACSFile |
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| diff -r 7a910b2c72ff -r 0eaa8225a09a chipsequtil/map_to_known_genes.xml --- a/chipsequtil/map_to_known_genes.xml Wed Mar 30 15:22:19 2016 -0400 +++ b/chipsequtil/map_to_known_genes.xml Mon Apr 04 14:52:14 2016 -0400 |
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| @@ -31,12 +31,11 @@ <param name="tss" checked="true" label="calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" /> <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false"> - <option value="auto">auto</option> <option value="MACS">MACS</option> <option selected="true" value="BED">BED</option> </param> - <param name="detail" checked="false" label="Add extra fields to output" type="boolean" truevalue="--detail" falsevalue="" help="" /> + <param name="detail" checked="true" label="Add extra fields to output" type="boolean" truevalue="--detail" falsevalue="" help="" /> <param name="intergenic" checked="false" label="Write intergenic peaks to the gene file as well with None as gene ID" type="boolean" truevalue="--intergenic" falsevalue="" help="" /> </inputs> <outputs> |