Mercurial > repos > iuc > lofreq_alnqual

comparison lofreq_alnqual.xml @ 6:82dcad2f4e4b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
author iuc
date Wed, 06 Jul 2022 09:23:15 +0000
parents 2ea2d74268ad
children
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5:2ea2d74268ad 6:82dcad2f4e4b
1 <tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@TOOL_VERSION@+galaxy0" profile="18.01"> 1 <tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@TOOL_VERSION@+galaxy1" profile="18.01">
2 <description>to aligned read SAM/BAM records</description> 2 <description>to aligned read SAM/BAM records</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
21 <tests> 21 <tests>
22 <test> 22 <test>
23 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 23 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
24 <param name="ref_selector" value="history" /> 24 <param name="ref_selector" value="history" />
25 <param name="ref" ftype="fasta" value="pBR322.fa" /> 25 <param name="ref" ftype="fasta" value="pBR322.fa" />
26 <output name="output" file="alnqual-out1.bam" /> 26 <output name="output" file="alnqual-out1.bam" ftype="bam" />
27 </test> 27 </test>
28 <test> 28 <test>
29 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 29 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
30 <param name="ref_selector" value="history" /> 30 <param name="ref_selector" value="history" />
31 <param name="ref" ftype="fasta" value="pBR322.fa" /> 31 <param name="ref" ftype="fasta" value="pBR322.fa" />
32 <conditional name="alnqual_choice"> 32 <conditional name="alnqual_choice">
33 <param name="alnquals_to_use" value="-B" /> 33 <param name="alnquals_to_use" value="-B" />
34 </conditional> 34 </conditional>
35 <output name="output" file="alnqual-out2.bam" /> 35 <output name="output" file="alnqual-out2.bam" ftype="bam" />
36 </test> 36 </test>
37 <test> 37 <test>
38 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 38 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
39 <param name="ref_selector" value="history" /> 39 <param name="ref_selector" value="history" />
40 <param name="ref" ftype="fasta" value="pBR322.fa" /> 40 <param name="ref" ftype="fasta" value="pBR322.fa" />
41 <conditional name="alnqual_choice"> 41 <conditional name="alnqual_choice">
42 <param name="alnquals_to_use" value="-A" /> 42 <param name="alnquals_to_use" value="-A" />
43 </conditional> 43 </conditional>
44 <output name="output" file="alnqual-out3.bam" /> 44 <output name="output" file="alnqual-out3.bam" ftype="bam" />
45 </test> 45 </test>
46 <test> 46 <test>
47 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 47 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
48 <param name="ref_selector" value="history" /> 48 <param name="ref_selector" value="history" />
49 <param name="ref" ftype="fasta" value="pBR322.fa" /> 49 <param name="ref" ftype="fasta" value="pBR322.fa" />
50 <conditional name="alnqual_choice"> 50 <conditional name="alnqual_choice">
51 <param name="extended_baq" value="false" /> 51 <param name="extended_baq" value="false" />
52 </conditional> 52 </conditional>
53 <output name="output" file="alnqual-out4.bam" /> 53 <output name="output" file="alnqual-out4.bam" ftype="bam" />
54 </test> 54 </test>
55 <test> 55 <test>
56 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 56 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
57 <param name="ref_selector" value="history" /> 57 <param name="ref_selector" value="history" />
58 <param name="ref" ftype="fasta" value="pBR322.fa" /> 58 <param name="ref" ftype="fasta" value="pBR322.fa" />
59 <param name="recompute" value="true" /> 59 <param name="recompute" value="true" />
60 <output name="output" file="alnqual-out5.bam" /> 60 <output name="output" file="alnqual-out5.bam" ftype="bam" />
61 </test> 61 </test>
62 </tests> 62 </tests>
63 <help><![CDATA[ 63 <help><![CDATA[
64 lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to 64 lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to
65 aligned read records 65 aligned read records