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planemo upload commit 49a2861a9b3480ea25f1e5526d2edf9dc8cb5334
author iuc
date Sun, 11 Aug 2024 21:06:06 +0000
parents 341246805ea1
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0:341246805ea1 1:16eccd223c6e
1 <tool id="basil" name="basil" version="1.2.0"> 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>
4 <token name="@TOOL_VERSION@">1.2.0</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="1.2.0">anise_basil</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">anise_basil</requirement>
5 </requirements> 9 </requirements>
6 <version_command>basil --version 2>&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>
7 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
8 ln -s '$ref' 'ref.fa' && 12 #if $reference_source.reference_source_selector == 'history':
13 ln -f -s '$reference_source.ref' ref.fa &&
14 #else:
15 ln -f -s '$reference_source.ref.fields.path' ref.fa &&
16 #end if
9 ln -s '$bam' 'in.bam' && 17 ln -s '$bam' 'in.bam' &&
10 ln -s '$vcf' 'out.vcf' && 18 ln -s '$vcf' 'out.vcf' &&
11 basil 19 basil
12 --input-reference 'ref.fa' 20 --input-reference 'ref.fa'
13 --input-mapping 'in.bam' 21 --input-mapping 'in.bam'
14 --out-vcf 'out.vcf' 22 --out-vcf 'out.vcf'
15 --oea-min-support-each-side '$min_oea_each_side' 23 --oea-min-support-each-side '$min_oea_each_side'
16 ]]></command> 24 ]]></command>
17 <inputs> 25 <inputs>
18 <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/> 26 <conditional name="reference_source">
27 <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
28 <option value="cached">Use a built-in genome index</option>
29 <option value="history">Use a genome from history and build index</option>
30 </param>
31 <when value="cached">
32 <param name="ref" type="select" label="Using reference genome" help="Select genome from the list">
33 <options from_data_table="all_fasta">
34 <filter type="sort_by" column="2"/>
35 <validator type="no_options" message="No reference genomes are available"/>
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"/>
38 </param>
39 </when>
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."/>
42 </when>
43 </conditional>
19 <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."/>
20 <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."/>
21 </inputs> 46 </inputs>
22 <outputs> 47 <outputs>
23 <data name="vcf" format="vcf" /> 48 <data name="vcf" format="vcf"/>
24 </outputs> 49 </outputs>
25 <tests> 50 <tests>
26 <test> 51 <test>
52 <conditional name="reference_source">
53 <param name="reference_source_selector" value="history" />
54 <param name="ref" ftype="fasta" value="ref.fa"/>
55 </conditional>
27 <param name="ref" value="ref.fa"/> 56 <param name="ref" value="ref.fa"/>
28 <param name="bam" value="simulated.bam"/> 57 <param name="bam" value="simulated.bam"/>
29 <param name="min_oea_each_side" value="2"/> 58 <param name="min_oea_each_side" value="2"/>
59 <output name="vcf" file="basil.vcf"/>
60 </test>
61 <test>
62 <conditional name="reference_source">
63 <param name="reference_source_selector" value="cached" />
64 <param name="ref" value="genome"/>
65 </conditional>
66 <param name="bam" value="simulated.bam"/>
67 <param name="min_oea_each_side" value="2"/>
30 <output name="vcf" file="basil.vcf"/> 68 <output name="vcf" file="basil.vcf"/>
31 </test> 69 </test>
32 </tests> 70 </tests>
33 <help><![CDATA[ 71 <help><![CDATA[
34 BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. Use BASIL to analyze BAM files for tentative insertion sites. 72 BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. Use BASIL to analyze BAM files for tentative insertion sites.