Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.xml @ 13:02bf6425fc25 draft

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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 14:18:57 +0000
parents 7a418148319d
children 6f4c61123a36
comparison
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12:7a418148319d 13:02bf6425fc25
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="2.0.1" profile="19.01"> 2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.0.2" 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">
18 --thresh '$thresh' 18 --thresh '$thresh'
19 --phred '$phred' 19 --phred '$phred'
20 --trim '$trim' 20 --trim '$trim'
21 $chimera_correction 21 $chimera_correction
22 --outputFile '$output_xlsx' 22 --outputFile '$output_xlsx'
23 --outputFile_csv '$outputFile_csv'
23 --outputFile2 '$output_xlsx2' 24 --outputFile2 '$output_xlsx2'
24 --outputFile3 '$output_xlsx3' 25 --outputFile3 '$output_xlsx3'
25 ]]> 26 ]]>
26 </command> 27 </command>
27 <inputs> 28 <inputs>
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."/> 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="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."/>
36 </inputs> 37 </inputs>
37 <outputs> 38 <outputs>
38 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> 39 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
40 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
39 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> 41 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
40 <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/> 42 <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
41 </outputs> 43 </outputs>
42 <tests> 44 <tests>
43 <test> 45 <test>
48 <param name="thresh" value="0"/> 50 <param name="thresh" value="0"/>
49 <param name="phred" value="20"/> 51 <param name="phred" value="20"/>
50 <param name="trim" value="10"/> 52 <param name="trim" value="10"/>
51 <param name="chimera_correction" value="True"/> 53 <param name="chimera_correction" value="True"/>
52 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> 54 <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"/>
53 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> 56 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
54 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/> 57 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
55 </test> 58 </test>
56 </tests> 59 </tests>
57 <help> <![CDATA[ 60 <help> <![CDATA[