| Previous changeset 0:44519e762f16 (2017-01-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit ab4afb50e6c991cc2e784a93a0c7a75329eac88c |
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modified:
fermikit_run_calling.xml |
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| diff -r 44519e762f16 -r ed056d243455 fermikit_run_calling.xml --- a/fermikit_run_calling.xml Thu Jan 05 08:35:48 2017 -0500 +++ b/fermikit_run_calling.xml Mon Jun 27 11:22:33 2022 +0000 |
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| @@ -1,13 +1,23 @@ -<tool id="fermikit_variants" name="fermikit-variants" version="0.14.dev1"> +<tool id="fermikit_variants" name="fermikit-variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>call variants from genome-aligned contigs</description> + <macros> + <token name="@TOOL_VERSION@">0.14.dev1</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> <requirements> - <requirement type="package" version="0.14.dev1">fermikit</requirement> + <requirement type="package" version="@TOOL_VERSION@">fermikit</requirement> <requirement type="package" version="0.6.5">sambamba</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($bam.element_identifier)) - #set ref = $reference_genome.fasta_item.fields.path if $reference_genome.reference_genome_source == "reference" else $reference_genome.history_item + + #if $reference_genome.reference_genome_source == "reference" + #set ref=$reference_genome.fasta_item.fields.path + #else + ln -s '$reference_genome.history_item' reference.fa && + #set ref="reference.fa" + #end if export ROOT=\$(dirname \$(type -P k8)) && ln -f -s '$bam' '$escaped_element_identifier' && htsbox pileup -cuf '$ref' '$escaped_element_identifier' | gzip -1 > raw.vcf.gz && |