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planemo upload commit beceb2f899abad7217eb72f57f6985c4ad4c17a8
author iuc
date Fri, 18 Jul 2025 08:43:41 +0000
parents 77fc7640abc7
children
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1:77fc7640abc7 2:bf1bdb62d882
1 <tool id="basil" name="basil" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> 1 <tool id="basil" name="basil" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>Breakpoint detection, including large insertions</description> 2 <description>Breakpoint detection, including large insertions</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.2.0</token> 4 <token name="@TOOL_VERSION@">1.2.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">anise_basil</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">anise_basil</requirement>
9 </requirements> 9 </requirements>
10 <version_command>basil --version 2&gt;&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command> 10 <version_command>basil --version 2&gt;&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command>
36 </options> 36 </options>
37 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 37 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
38 </param> 38 </param>
39 </when> 39 </when>
40 <when value="history"> 40 <when value="history">
41 <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/> 41 <param name="ref" argument="--input-reference" type="data" format="fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
42 </when> 42 </when>
43 </conditional> 43 </conditional>
44 <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/> 44 <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/>
45 <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion. In range [1..inf]. This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered."/> 45 <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion. In range [1..inf]. This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered."/>
46 </inputs> 46 </inputs>
51 <test> 51 <test>
52 <conditional name="reference_source"> 52 <conditional name="reference_source">
53 <param name="reference_source_selector" value="history" /> 53 <param name="reference_source_selector" value="history" />
54 <param name="ref" ftype="fasta" value="ref.fa"/> 54 <param name="ref" ftype="fasta" value="ref.fa"/>
55 </conditional> 55 </conditional>
56 <param name="ref" value="ref.fa"/>
57 <param name="bam" value="simulated.bam"/> 56 <param name="bam" value="simulated.bam"/>
58 <param name="min_oea_each_side" value="2"/> 57 <param name="min_oea_each_side" value="2"/>
59 <output name="vcf" file="basil.vcf"/> 58 <output name="vcf" file="basil.vcf"/>
60 </test> 59 </test>
61 <test> 60 <test>