Mercurial > repos > iuc > crossmap_bed
changeset 9:ee86b27291b5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
| author | iuc |
|---|---|
| date | Thu, 20 Jan 2022 04:31:56 +0000 |
| parents | f4a70882a71b |
| children | 50b7875a49d0 |
| files | crossmap_bed.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, 27 insertions(+), 19 deletions(-) [+] |
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--- a/crossmap_bed.xml Thu Jul 15 16:19:05 2021 +0000 +++ b/crossmap_bed.xml Thu Jan 20 04:31:56 2022 +0000 @@ -18,15 +18,15 @@ <command><![CDATA[ CrossMap.py bed '${chain_source.input_chain}' - '${input}' #if $merge_unmapped_entries: > '${output_combined}' #else: output + --unmap-file output.unmap #end if - +--chromid $chromid ]]></command> @@ -35,7 +35,11 @@ help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/> <expand macro="chain" /> - + <param name="chromid" type="select" label="Style of chromosome IDs"> + <option value="a" selected="true">As-is</option> + <option value="l">Long style, e.g. chr1, chrX</option> + <option value="s">Short style, e.g. 1, X</option> + </param> <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/> </inputs> @@ -76,6 +80,7 @@ <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="txt"/> <param name="merge_unmapped_entries" value="false" /> + <param name="chromid" value="s" /> <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/> <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/> @@ -85,6 +90,7 @@ <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="txt"/> <param name="merge_unmapped_entries" value="true" /> + <param name="chromid" value="s" /> <output name="output_combined" file="test_bed_02_output_a__all.bed"/> </test>
--- a/macros.xml Thu Jul 15 16:19:05 2021 +0000 +++ b/macros.xml Thu Jan 20 04:31:56 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 16:19:05 2021 +0000 +++ b/test-data/test_bed_02_input_a.bed Thu Jan 20 04:31:56 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 16:19:05 2021 +0000 +++ b/test-data/test_bed_02_output_a__all.bed Thu Jan 20 04:31:56 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 16:19:05 2021 +0000 +++ b/test-data/test_bed_02_output_a__only_fails.bed Thu Jan 20 04:31:56 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 16:19:05 2021 +0000 +++ b/test-data/test_vcf_01_input.vcf Thu Jan 20 04:31:56 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 16:19:05 2021 +0000 +++ b/test-data/test_vcf_01_output.vcf.unmap Thu Jan 20 04:31:56 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)