Mercurial > repos > iuc > crossmap_vcf
changeset 10:d4965adac10c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author | iuc |
---|---|
date | Mon, 02 Sep 2024 12:01:12 +0000 |
parents | 18f7e96459d2 |
children | |
files | crossmap_vcf.xml macros.xml |
diffstat | 2 files changed, 8 insertions(+), 18 deletions(-) [+] |
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--- a/crossmap_vcf.xml Thu Jan 20 04:32:23 2022 +0000 +++ b/crossmap_vcf.xml Mon Sep 02 12:01:12 2024 +0000 @@ -6,13 +6,12 @@ <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ #set $input_file = str($seq_source.input) ln -s '${seq_source.input_fasta}' 'genome.fasta' && -CrossMap.py vcf +CrossMap vcf #if $seq_source.index_source_s == "cached" ## This is the 2nd dbkey, and the corresponding value has to be looked up @@ -26,7 +25,6 @@ $no_comp_alleles output ]]></command> - <inputs> <conditional name="seq_source"> <param name="index_source_s" type="select" label="Source for Input Data"> @@ -45,25 +43,20 @@ <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file"> <options from_data_table="all_fasta"/> </param> - - <expand macro="chain" /> + <expand macro="chain"/> </when> - <when value="history"> <param name="input" type="data" format="vcf" label="VCF file"/> <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/> - - <expand macro="chain" /> + <expand macro="chain"/> </when> </conditional> <param argument="--no-comp-alleles" type="boolean" truevalue="" falsevalue="--no-comp-alleles" checked="true" label="Check if the reference allele is different from the alternate allele"/> </inputs> - <outputs> - <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" /> - <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" /> + <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output"/> + <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap"/> </outputs> - <tests> <test> <param name="index_source_s" value="history"/> @@ -71,11 +64,10 @@ <param name="index_source" value="history"/> <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/> <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/> - <output name="output"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_text_matching expression="##liftOverProgram=<CrossMap,version=[0-9.]+,website=https://sourceforge.net/projects/crossmap>"/> + <has_text_matching expression="##liftOverProgram=CrossMap,version=[0-9.]+,website=https://crossmap.readthedocs.io/en/latest"/> <has_text text="##targetRefGenome="/> <has_text text="#CHROM"/> <has_text_matching expression="2.*?rs11449.*?PASS"/> @@ -108,7 +100,6 @@ - In the output VCF file, whether the chromosome IDs contain “chr” or not depends on the format of the input VCF file. ]]></help> - <citations> <citation type="doi">10.1093/bioinformatics/btt730</citation> </citations>
--- a/macros.xml Thu Jan 20 04:32:23 2022 +0000 +++ b/macros.xml Mon Sep 02 12:01:12 2024 +0000 @@ -1,4 +1,3 @@ -<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> @@ -6,7 +5,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.6.1</token> + <token name="@TOOL_VERSION@">0.7.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="stdio"> <stdio> @@ -17,7 +16,7 @@ </xml> <xml name="version_command"> <version_command><![CDATA[ -CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' +CrossMap 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' ]]></version_command> </xml> <xml name="chain">