Mercurial > repos > mheinzl > variant_analyzer2
changeset 16:30aec05d04d3 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Mon, 22 Feb 2021 14:33:12 +0000 |
| parents | 6f4c61123a36 |
| children | f06067bedfc5 |
| files | read2mut.py read2mut.xml |
| diffstat | 2 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/read2mut.py Mon Feb 22 14:30:58 2021 +0000 +++ b/read2mut.py Mon Feb 22 14:33:12 2021 +0000 @@ -64,7 +64,7 @@ parser.add_argument('--chimera_correction', action="store_true", help='Count chimeric variants and correct the variant frequencies') parser.add_argument('--delim_csv', type=str, default=",", - help='Deliminator in csv summary file. Default comma.') + help='Delimiter in csv summary file. Default comma.') return parser
--- a/read2mut.xml Mon Feb 22 14:30:58 2021 +0000 +++ b/read2mut.xml Mon Feb 22 14:33:12 2021 +0000 @@ -23,6 +23,7 @@ --outputFile_csv '$outputFile_csv' --outputFile2 '$output_xlsx2' --outputFile3 '$output_xlsx3' + --delim_csv '$delim_csv' ]]> </command> <inputs> @@ -34,7 +35,7 @@ <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/> <param name="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10."/> <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/> - <param name="delim_csv" type="string" label="Delimiter in csv file" value="," help="Delimiter in csv summary file. Default = comma."/> + <param name="delim_csv" type="text" label="Delimiter in csv file" value="," help="Delimiter in csv summary file. Default = comma."/> </inputs> <outputs> <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>