Mercurial > repos > mheinzl > variant_analyzer2
changeset 12:7a418148319d draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Tue, 16 Feb 2021 07:08:25 +0000 |
| parents | 84a1a3f70407 |
| children | 02bf6425fc25 |
| files | read2mut.py read2mut.xml |
| diffstat | 2 files changed, 16 insertions(+), 4 deletions(-) [+] |
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--- a/read2mut.py Mon Feb 15 21:53:24 2021 +0000 +++ b/read2mut.py Tue Feb 16 07:08:25 2021 +0000 @@ -46,7 +46,11 @@ parser.add_argument('--sscsJson', help='JSON file with SSCS counts collected by mut2sscs.py.') parser.add_argument('--outputFile', - help='Output xlsx file of mutation details.') + help='Output xlsx file with summary of mutations.') + parser.add_argument('--outputFile2', + help='Output xlsx file with allele frequencies of mutations.') + parser.add_argument('--outputFile3', + help='Output xlsx file with examples of the tier classification.') parser.add_argument('--thresh', type=int, default=0, help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.') parser.add_argument('--phred', type=int, default=20, @@ -72,6 +76,8 @@ json_file = args.inputJson sscs_json = args.sscsJson outfile = args.outputFile + outfile2 = args.outputFile2 + outfile3 = args.outputFile3 thresh = args.thresh phred_score = args.phred trim = args.trim
--- a/read2mut.xml Mon Feb 15 21:53:24 2021 +0000 +++ b/read2mut.xml Tue Feb 16 07:08:25 2021 +0000 @@ -20,6 +20,8 @@ --trim '$trim' $chimera_correction --outputFile '$output_xlsx' + --outputFile2 '$output_xlsx2' + --outputFile3 '$output_xlsx3' ]]> </command> <inputs> @@ -33,7 +35,9 @@ <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."/> </inputs> <outputs> - <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/> + <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> + <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> + <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/> </outputs> <tests> <test> @@ -45,7 +49,9 @@ <param name="phred" value="20"/> <param name="trim" value="10"/> <param name="chimera_correction" value="True"/> - <output name="output_xlsx" file="Variant_Analyzer_test.xlsx" decompress="true" lines_diff="2"/> + <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> + <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> + <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/> </test> </tests> <help> <![CDATA[ @@ -74,7 +80,7 @@ **Output** -The output is an XLSX file containing frequencies stats for DCS mutations based +The output are three XLSX files containing frequencies stats for DCS mutations based on information from the raw reads. In addition to that a tier based classification is provided based on the amout of support for a true variant call.