Mercurial > repos > iuc > vsnp_add_zero_coverage
changeset 4:e12ccc57875c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit a80e3713d10fafef22e964198d59251adf955812"
| author | iuc |
|---|---|
| date | Thu, 14 Jan 2021 09:11:12 +0000 |
| parents | 2e863710a2f0 |
| children | 5a5cf6f024bf |
| files | vsnp_add_zero_coverage.xml vsnp_determine_ref_from_data.py |
| diffstat | 2 files changed, 7 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/vsnp_add_zero_coverage.xml Thu Dec 10 15:26:25 2020 +0000 +++ b/vsnp_add_zero_coverage.xml Thu Jan 14 09:11:12 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.1" profile="@PROFILE@"> +<tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.2" profile="@PROFILE@"> <description></description> <macros> <import>macros.xml</import> @@ -37,7 +37,7 @@ <when value="cached"> <param name="reference" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> - <filter type="data_meta" column="dbkey" key="dbkey" ref="bam_input"/> + <filter type="data_meta" column="1" key="dbkey" ref="bam_input"/> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file"/> </options> </param>
--- a/vsnp_determine_ref_from_data.py Thu Dec 10 15:26:25 2020 +0000 +++ b/vsnp_determine_ref_from_data.py Thu Jan 14 09:11:12 2021 +0000 @@ -197,12 +197,12 @@ if __name__ == '__main__': parser = argparse.ArgumentParser() - parser.add_argument('--dnaprint_fields', action='append', dest='dnaprint_fields', nargs=2, required=False, default=None, help="List of dnaprints data table value, name and path fields") - parser.add_argument('--read1', action='store', dest='read1', required=True, default=None, help='Required: single read') + parser.add_argument('--dnaprint_fields', action='append', dest='dnaprint_fields', nargs=2, help="List of dnaprints data table value, name and path fields") + parser.add_argument('--read1', action='store', dest='read1', help='Required: single read') parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read') - parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Input files are gzipped') - parser.add_argument('--output_dbkey', action='store', dest='output_dbkey', required=True, default=None, help='Output reference file') - parser.add_argument('--output_metrics', action='store', dest='output_metrics', required=True, default=None, help='Output metrics file') + parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped') + parser.add_argument('--output_dbkey', action='store', dest='output_dbkey', help='Output reference file') + parser.add_argument('--output_metrics', action='store', dest='output_metrics', help='Output metrics file') args = parser.parse_args()