Mercurial > repos > iuc > crossmap_region
changeset 1:eb66d7a04bf8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
| author | iuc |
|---|---|
| date | Thu, 20 Jan 2022 04:31:00 +0000 |
| parents | 8635b6b8a8f2 |
| children | a50ef4d58c90 |
| files | crossmap_region.xml macros.xml test-data/test_bam_01_output_a.bam test-data/test_bed_02_input_a.bed test-data/test_bed_02_output_a__all.bed test-data/test_bed_02_output_a__only_fails.bed test-data/test_vcf_01_input.vcf test-data/test_vcf_01_output.vcf.unmap |
| diffstat | 8 files changed, 25 insertions(+), 17 deletions(-) [+] |
line wrap: on
line diff
--- a/crossmap_region.xml Thu Jul 15 16:19:33 2021 +0000 +++ b/crossmap_region.xml Thu Jan 20 04:31:00 2022 +0000 @@ -10,14 +10,20 @@ CrossMap.py region '${chain_source.input_chain}' '${input}' + $output + --chromid $chromid --ratio $ratio - '$output' ]]></command> <inputs> <param name="input" type="data" format="bed" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/> <expand macro="chain" /> <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/> + <param argument="--chromid" type="select" label="Chromid" help="The style of chromosome IDs"> + <option value="a" selected="true">Default (a)</option> + <option value="s">Short style (s)</option> + <option value="l">Long stype (l)</option> + </param> </inputs> <outputs> <data name="output" format="bed"/>
--- a/macros.xml Thu Jul 15 16:19:33 2021 +0000 +++ b/macros.xml Thu Jan 20 04:31:00 2022 +0000 @@ -6,7 +6,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.5.2</token> + <token name="@TOOL_VERSION@">0.6.1</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="stdio"> <stdio>
--- a/test-data/test_bed_02_input_a.bed Thu Jul 15 16:19:33 2021 +0000 +++ b/test-data/test_bed_02_input_a.bed Thu Jan 20 04:31:00 2022 +0000 @@ -1,5 +1,5 @@ -chr1 100 10000 -chr2 100 10000 -chr3 100 10000 -chr4 8941700 8947200 -chr5 1 100000000 \ No newline at end of file +1 100 10000 +2 100 10000 +3 100 10000 +4 8941700 8947200 +5 1 100000000
--- a/test-data/test_bed_02_output_a__all.bed Thu Jul 15 16:19:33 2021 +0000 +++ b/test-data/test_bed_02_output_a__all.bed Thu Jan 20 04:31:00 2022 +0000 @@ -1,5 +1,5 @@ -chr1 100 10000 Unmap -chr2 100 10000 Unmap -chr3 100 10000 Unmap -chr4 8941700 8947200 Unmap -chr5 1 100000000 Unmap +1 100 10000 Unmap +2 100 10000 Unmap +3 100 10000 Unmap +4 8941700 8947200 Unmap +5 1 100000000 Unmap
--- a/test-data/test_bed_02_output_a__only_fails.bed Thu Jul 15 16:19:33 2021 +0000 +++ b/test-data/test_bed_02_output_a__only_fails.bed Thu Jan 20 04:31:00 2022 +0000 @@ -1,5 +1,5 @@ -chr1 100 10000 Unmap -chr2 100 10000 Unmap -chr3 100 10000 Unmap -chr4 8941700 8947200 Unmap -chr5 1 100000000 Unmap +1 100 10000 Unmap +2 100 10000 Unmap +3 100 10000 Unmap +4 8941700 8947200 Unmap +5 1 100000000 Unmap
--- a/test-data/test_vcf_01_input.vcf Thu Jul 15 16:19:33 2021 +0000 +++ b/test-data/test_vcf_01_input.vcf Thu Jan 20 04:31:00 2022 +0000 @@ -2,6 +2,7 @@ ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype"> ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities"> ##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods"> +##contig=<ID=1,length=195471971> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMP001 SAMP002 1 10 rs11449 G A . PASS . GT 0/0 0/1 1 100 rs84825 C C . PASS . GT:GP 0/1:. 0/1:0.03,0.97,0
--- a/test-data/test_vcf_01_output.vcf.unmap Thu Jul 15 16:19:33 2021 +0000 +++ b/test-data/test_vcf_01_output.vcf.unmap Thu Jan 20 04:31:00 2022 +0000 @@ -2,5 +2,6 @@ ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype"> ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities"> ##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods"> +##contig=<ID=1,length=195471971> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMP001 SAMP002 1 200 rs84823 T G . PASS . GT:PL ./.:. 1/1:10,5,0 Fail(REF==ALT)