| Previous changeset 6:b21851ddcc79 (2020-09-30) Next changeset 8:6e96c77f5824 (2021-11-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7" |
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modified:
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 |
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added:
test-data/test_region.bed |
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| diff -r b21851ddcc79 -r 71730c177cdf crossmap_vcf.xml --- a/crossmap_vcf.xml Wed Sep 30 13:59:28 2020 +0000 +++ b/crossmap_vcf.xml Thu Jul 15 16:20:06 2021 +0000 |
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| @@ -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"/> |
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| diff -r b21851ddcc79 -r 71730c177cdf macros.xml --- a/macros.xml Wed Sep 30 13:59:28 2020 +0000 +++ b/macros.xml Thu Jul 15 16:20:06 2021 +0000 |
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| @@ -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"/> |
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| diff -r b21851ddcc79 -r 71730c177cdf test-data/test_bam_01_output_a.bam |
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| Binary file test-data/test_bam_01_output_a.bam has changed |
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| diff -r b21851ddcc79 -r 71730c177cdf test-data/test_bed_02_output_a__all.bed --- 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 |
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| @@ -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 |
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| diff -r b21851ddcc79 -r 71730c177cdf test-data/test_bed_02_output_a__only_fails.bed --- 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 |
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| @@ -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 |
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| diff -r b21851ddcc79 -r 71730c177cdf test-data/test_bigwig_01_output_a.bw |
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| Binary file test-data/test_bigwig_01_output_a.bw has changed |
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| diff -r b21851ddcc79 -r 71730c177cdf test-data/test_region.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_region.bed Thu Jul 15 16:20:06 2021 +0000 |
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| @@ -0,0 +1,2 @@ +chr2 90000 990000 map_ratio=1.0000 +chr3 75000 975000 map_ratio=1.0000 |