Mercurial > repos > iuc > crossmap_vcf
changeset 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 | b21851ddcc79 |
| children | 6e96c77f5824 |
| files | crossmap_vcf.xml macros.xml test-data/test_bam_01_output_a.bam test-data/test_bed_02_output_a__all.bed test-data/test_bed_02_output_a__only_fails.bed test-data/test_bigwig_01_output_a.bw test-data/test_region.bed |
| diffstat | 7 files changed, 19 insertions(+), 16 deletions(-) [+] |
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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"/>
--- a/macros.xml Wed Sep 30 13:59:28 2020 +0000 +++ b/macros.xml Thu Jul 15 16:20:06 2021 +0000 @@ -6,8 +6,8 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.3.7</token> - <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token> + <token name="@TOOL_VERSION@">0.5.2</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="stdio"> <stdio> <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
--- a/test-data/test_bed_02_output_a__all.bed Wed Sep 30 13:59:28 2020 +0000 +++ b/test-data/test_bed_02_output_a__all.bed Thu Jul 15 16:20:06 2021 +0000 @@ -1,5 +1,5 @@ -chr1 100 10000 Fail -chr2 100 10000 Fail -chr3 100 10000 Fail -chr4 8941700 8947200 Fail -chr5 1 100000000 Fail +chr1 100 10000 Unmap +chr2 100 10000 Unmap +chr3 100 10000 Unmap +chr4 8941700 8947200 Unmap +chr5 1 100000000 Unmap
--- a/test-data/test_bed_02_output_a__only_fails.bed Wed Sep 30 13:59:28 2020 +0000 +++ b/test-data/test_bed_02_output_a__only_fails.bed Thu Jul 15 16:20:06 2021 +0000 @@ -1,5 +1,5 @@ -chr1 100 10000 -chr2 100 10000 -chr3 100 10000 -chr4 8941700 8947200 -chr5 1 100000000 +chr1 100 10000 Unmap +chr2 100 10000 Unmap +chr3 100 10000 Unmap +chr4 8941700 8947200 Unmap +chr5 1 100000000 Unmap