Mercurial > repos > iuc > crossmap_vcf
diff crossmap_vcf.xml @ 7:71730c177cdf draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
| author | iuc |
|---|---|
| date | Thu, 15 Jul 2021 16:20:06 +0000 |
| parents | 9d61d74f03a4 |
| children | 6e96c77f5824 |
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--- a/crossmap_vcf.xml Wed Sep 30 13:59:28 2020 +0000 +++ b/crossmap_vcf.xml Thu Jul 15 16:20:06 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@"> +<tool id="crossmap_vcf" name="CrossMap VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>Convert genome coordinates or annotation files between genome assemblies</description> <macros> <import>macros.xml</import> @@ -21,7 +21,7 @@ '${input_file}' '${seq_source.input_fasta}' - +$no_comp_alleles output ]]></command> @@ -54,6 +54,7 @@ <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> @@ -72,8 +73,8 @@ <output name="output"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/> - <has_text text="##new_reference_genome="/> + <has_text_matching expression="##liftOverProgram=<CrossMap,version=[0-9.]+,website=https://sourceforge.net/projects/crossmap>"/> + <has_text text="##targetRefGenome="/> <has_text text="#CHROM"/> <has_text_matching expression="2.*?rs11449.*?PASS"/> <has_text_matching expression="2.*?rs84825.*?PASS"/>