Mercurial > repos > mheinzl > variant_analyzer2
changeset 17:f06067bedfc5 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 14:40:07 +0000 |
| parents | 30aec05d04d3 |
| children | d910b6dfd826 |
| files | read2mut.py read2mut.xml |
| diffstat | 2 files changed, 1 insertions(+), 8 deletions(-) [+] |
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--- a/read2mut.py Mon Feb 22 14:33:12 2021 +0000 +++ b/read2mut.py Mon Feb 22 14:40:07 2021 +0000 @@ -63,10 +63,6 @@ help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.') 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='Delimiter in csv summary file. Default comma.') - - return parser @@ -238,7 +234,7 @@ pure_tags_dict_short = pure_tags_dict csv_data = open(outputFile_csv, "w") - csv_writer = csv.writer(csv_data, delimiter=delim_csv) + csv_writer = csv.writer(csv_data, delimiter=",") # output summary with threshold workbook = xlsxwriter.Workbook(outfile)
--- a/read2mut.xml Mon Feb 22 14:33:12 2021 +0000 +++ b/read2mut.xml Mon Feb 22 14:40:07 2021 +0000 @@ -23,7 +23,6 @@ --outputFile_csv '$outputFile_csv' --outputFile2 '$output_xlsx2' --outputFile3 '$output_xlsx3' - --delim_csv '$delim_csv' ]]> </command> <inputs> @@ -35,7 +34,6 @@ <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="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"/> @@ -53,7 +51,6 @@ <param name="phred" value="20"/> <param name="trim" value="10"/> <param name="delim_csv" value=","/> - <param name="chimera_correction" value="True"/> <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/> <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>