Mercurial > repos > iuc > fermikit_variants

comparison fermikit_run_calling.xml @ 1:4c52b134a42f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit ab4afb50e6c991cc2e784a93a0c7a75329eac88c
author iuc
date Mon, 27 Jun 2022 11:21:40 +0000
parents 96bf82df80c6
children
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0:96bf82df80c6 1:4c52b134a42f
1 <tool id="fermikit_variants" name="fermikit-variants" version="0.14.dev1"> 1 <tool id="fermikit_variants" name="fermikit-variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>call variants from genome-aligned contigs</description> 2 <description>call variants from genome-aligned contigs</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.14.dev1</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="0.14.dev1">fermikit</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">fermikit</requirement>
5 <requirement type="package" version="0.6.5">sambamba</requirement> 9 <requirement type="package" version="0.6.5">sambamba</requirement>
6 </requirements> 10 </requirements>
7 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
8 #import re 12 #import re
9 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($bam.element_identifier)) 13 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
10 #set ref = $reference_genome.fasta_item.fields.path if $reference_genome.reference_genome_source == "reference" else $reference_genome.history_item 14
15 #if $reference_genome.reference_genome_source == "reference"
16 #set ref=$reference_genome.fasta_item.fields.path
17 #else
18 ln -s '$reference_genome.history_item' reference.fa &&
19 #set ref="reference.fa"
20 #end if
11 export ROOT=\$(dirname \$(type -P k8)) && 21 export ROOT=\$(dirname \$(type -P k8)) &&
12 ln -f -s '$bam' '$escaped_element_identifier' && 22 ln -f -s '$bam' '$escaped_element_identifier' &&
13 htsbox pileup -cuf '$ref' '$escaped_element_identifier' | gzip -1 > raw.vcf.gz && 23 htsbox pileup -cuf '$ref' '$escaped_element_identifier' | gzip -1 > raw.vcf.gz &&
14 k8 "\$ROOT"/hapdip.js deovlp raw.vcf.gz | k8 "\$ROOT"/hapdip.js anno | gzip -1 > tmp.vcf.gz 2> flt.vcf.log && 24 k8 "\$ROOT"/hapdip.js deovlp raw.vcf.gz | k8 "\$ROOT"/hapdip.js anno | gzip -1 > tmp.vcf.gz 2> flt.vcf.log &&
15 k8 "\$ROOT"/hapdip.js filter -q3 tmp.vcf.gz > flt.vcf 2>> flt.vcf.log && 25 k8 "\$ROOT"/hapdip.js filter -q3 tmp.vcf.gz > flt.vcf 2>> flt.vcf.log &&