Mercurial > repos > iuc > varscan_copynumber
changeset 10:9f8dbbbc0267 draft default tip
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 1232893782204bb041dd6ed46711295cb0bfc03f"
| author | iuc |
|---|---|
| date | Sat, 04 Dec 2021 22:23:36 +0000 |
| parents | 0bc56f894766 |
| children | |
| files | varscan.py varscan_copynumber.xml |
| diffstat | 2 files changed, 3 insertions(+), 6 deletions(-) [+] |
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--- a/varscan.py Fri Aug 16 15:50:10 2019 -0400 +++ b/varscan.py Sat Dec 04 22:23:36 2021 +0000 @@ -358,8 +358,7 @@ self.call, self.error ) else: - msg_header = '{0} failed.\n' - 'No further information about this error is available.\n\n'.format( + msg_header = '{0} failed.\nNo further information about this error is available.\n\n'.format( self.call ) return msg_header + self.message @@ -1045,8 +1044,8 @@ if mmqs_diff > max_mmqs_diff: record.filter.add('MMQSdiff') if ( - 1 - - alt_stats.avg_clipped_len + 1 + - alt_stats.avg_clipped_len / ref_stats.avg_clipped_len ) > max_relative_len_diff: record.filter.add('ReadLenDiff')
--- a/varscan_copynumber.xml Fri Aug 16 15:50:10 2019 -0400 +++ b/varscan_copynumber.xml Sat Dec 04 22:23:36 2021 +0000 @@ -41,8 +41,6 @@ <param argument="--data-ratio" name="data_ratio" type="float" value="1.0" min="0.0" max="1.0" label="The normal/tumor input data ratio for copynumber adjustment"/> - <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/> - </inputs> <outputs> <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/>