Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.xml @ 15:6f4c61123a36 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 14:30:58 +0000 |
| parents | 02bf6425fc25 |
| children | 30aec05d04d3 |
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| 14:bcdb63df70ce | 15:6f4c61123a36 |
|---|---|
| 1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.0.2" profile="17.01"> | 2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.0.3" profile="17.01"> |
| 3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> | 3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> |
| 4 <macros> | 4 <macros> |
| 5 <import>va_macros.xml</import> | 5 <import>va_macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements"> | 7 <expand macro="requirements"> |
| 32 <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/> | 32 <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/> |
| 33 <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/> | 33 <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/> |
| 34 <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."/> | 34 <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."/> |
| 35 <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."/> | 35 <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."/> |
| 36 <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."/> | 36 <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."/> |
| 37 <param name="delim_csv" type="string" label="Delimiter in csv file" value="," help="Delimiter in csv summary file. Default = comma."/> | |
| 37 </inputs> | 38 </inputs> |
| 38 <outputs> | 39 <outputs> |
| 39 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> | 40 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> |
| 40 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> | 41 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> |
| 41 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> | 42 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> |
| 48 <param name="file3" value="tag_count_dict_test.json"/> | 49 <param name="file3" value="tag_count_dict_test.json"/> |
| 49 <param name="file4" value="SSCS_counts_test.json"/> | 50 <param name="file4" value="SSCS_counts_test.json"/> |
| 50 <param name="thresh" value="0"/> | 51 <param name="thresh" value="0"/> |
| 51 <param name="phred" value="20"/> | 52 <param name="phred" value="20"/> |
| 52 <param name="trim" value="10"/> | 53 <param name="trim" value="10"/> |
| 54 <param name="delim_csv" value=","/> | |
| 53 <param name="chimera_correction" value="True"/> | 55 <param name="chimera_correction" value="True"/> |
| 54 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> | 56 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> |
| 55 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/> | 57 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/> |
| 56 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> | 58 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> |
| 57 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/> | 59 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/> |