Mercurial > repos > devteam > freebayes
changeset 34:a7c9782130e8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit be1c2e9e056710ef8b1110a121dc38c6e06dbbee"
author | iuc |
---|---|
date | Mon, 21 Feb 2022 09:53:39 +0000 |
parents | 04fa42777df9 |
children | a5937157062f |
files | freebayes.xml leftalign.xml macros.xml |
diffstat | 3 files changed, 10 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/freebayes.xml Fri Dec 03 22:27:40 2021 +0000 +++ b/freebayes.xml Mon Feb 21 09:53:39 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1"> +<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0"> <description>bayesian genetic variant detector</description> <xrefs> <xref type="bio.tools">freebayes</xref> @@ -8,8 +8,9 @@ </macros> <expand macro="requirements"> <requirement type="package" version="5.1.0">gawk</requirement> - <requirement type="package" version="20211022">parallel</requirement> + <requirement type="package" version="20211222">parallel</requirement> </expand> + <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ ##set up input files @@ -696,7 +697,7 @@ <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/> <param name="options_type_selector" value="simple"/> - <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" /> + <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" /> </test> </tests> <help><![CDATA[
--- a/leftalign.xml Fri Dec 03 22:27:40 2021 +0000 +++ b/leftalign.xml Mon Feb 21 09:53:39 2022 +0000 @@ -8,6 +8,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> + <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ ##set up input files #set $reference_fasta_filename = "localref.fa"
--- a/macros.xml Fri Dec 03 22:27:40 2021 +0000 +++ b/macros.xml Mon Feb 21 09:53:39 2022 +0000 @@ -1,12 +1,15 @@ <macros> - <token name="@TOOL_VERSION@">1.3.5</token> + <token name="@TOOL_VERSION@">1.3.6</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement> - <requirement type="package" version="1.12">samtools</requirement> + <requirement type="package" version="1.14">samtools</requirement> <yield /> </requirements> </xml> + <xml name="version_command"> + <version_command>freebayes --version | cut -d v -f 3</version_command> + </xml> <xml name="citations"> <citations> <citation type="bibtex">