Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.xml @ 27:5992e30ae50e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 16:56:05 +0000
parents cf6f0fb05bad
children afda74e874ac
comparison
equal deleted inserted replaced
26:5cb0bdd578cf 27:5992e30ae50e
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="2.0.4" profile="17.01"> 2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.0.1" profile="19.01">
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">
15 --bamFile bam_input.bam 15 --bamFile bam_input.bam
16 --inputJson '$file3' 16 --inputJson '$file3'
17 --sscsJson '$file4' 17 --sscsJson '$file4'
18 --thresh '$thresh' 18 --thresh '$thresh'
19 --phred '$phred' 19 --phred '$phred'
20 --trim5 '$trim5' 20 --trim '$trim'
21 --trim3 '$trim3'
22 $chimera_correction 21 $chimera_correction
23 --outputFile '$output_xlsx' 22 --outputFile '$output_xlsx'
24 --outputFile_csv '$outputFile_csv'
25 --outputFile2 '$output_xlsx2' 23 --outputFile2 '$output_xlsx2'
26 --outputFile3 '$output_xlsx3' 24 --outputFile3 '$output_xlsx3'
27 ]]> 25 ]]>
28 </command> 26 </command>
29 <inputs> 27 <inputs>
31 <param name="file2" type="data" format="bam" label="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/> 29 <param name="file2" type="data" format="bam" label="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/>
32 <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/> 30 <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/>
33 <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."/> 31 <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."/>
34 <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."/> 32 <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."/>
35 <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."/> 33 <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."/>
36 <param name="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at the beginning of reads to lower tier. Default 10."/> 34 <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."/>
37 <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at the end of reads to lower tier. Default 10."/>
38 <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."/> 35 <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."/>
39 </inputs> 36 </inputs>
40 <outputs> 37 <outputs>
41 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> 38 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
43 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> 39 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
44 <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/> 40 <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
45 </outputs> 41 </outputs>
46 <tests> 42 <tests>
47 <test> 43 <test>
49 <param name="file2" value="Interesting_Reads_test.trim.bam"/> 45 <param name="file2" value="Interesting_Reads_test.trim.bam"/>
50 <param name="file3" value="tag_count_dict_test.json"/> 46 <param name="file3" value="tag_count_dict_test.json"/>
51 <param name="file4" value="SSCS_counts_test.json"/> 47 <param name="file4" value="SSCS_counts_test.json"/>
52 <param name="thresh" value="0"/> 48 <param name="thresh" value="0"/>
53 <param name="phred" value="20"/> 49 <param name="phred" value="20"/>
54 <param name="trim5" value="10"/> 50 <param name="trim" value="10"/>
55 <param name="trim3" value="10"/> 51 <param name="chimera_correction" value="True"/>
56 <param name="delim_csv" value=","/>
57 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> 52 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
58 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/>
59 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> 53 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
60 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/> 54 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
61 </test> 55 </test>
62 </tests> 56 </tests>
63 <help> <![CDATA[ 57 <help> <![CDATA[