# HG changeset patch # User iuc # Date 1508431203 14400 # Node ID 37c8b1afc814a8a1d196261b37ab7d1e8e51ecbd # Parent af9e03d8577158df6a3a10550d2365b8be8e849e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1 diff -r af9e03d85771 -r 37c8b1afc814 crossmap_vcf.xml --- a/crossmap_vcf.xml Tue Sep 26 04:47:28 2017 -0400 +++ b/crossmap_vcf.xml Thu Oct 19 12:40:03 2017 -0400 @@ -8,70 +8,65 @@ - "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" - #else - "$chain_source.input_chain" - #end if +#if $seq_source.index_source_s == "cached" + ## This is the 2nd dbkey, and the corresponding value has to be looked up + "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" +#else + '${chain_source.input_chain}' +#end if - '${input_file}' - '${seq_source.input_fasta}' +'${input_file}' +'${seq_source.input_fasta}' - '${output}' +'${output}' - && mv "${output}.unmap" "$output_unmapped" +&& mv '${output}.unmap' '$output_unmapped' ]]> - - + + + + - + + - - - - - - - + - - + + - - - + + - - + - + - + @@ -93,25 +88,24 @@ VCF --- - VCF (variant call format) is a flexible and extendable line-oriented - text format developed by the 1000 Genome Project. It is useful for - representing single nucleotide variants, indels, copy number - variants, and structural variants. Chromosomes, coordinates, and - reference alleles are updated to a new assembly, and all the other - fields are not changed. +VCF (variant call format) is a flexible and extendable line-oriented +text format developed by the 1000 Genome Project. It is useful for +representing single nucleotide variants, indels, copy number +variants, and structural variants. Chromosomes, coordinates, and +reference alleles are updated to a new assembly, and all the other +fields are not changed. - NOTE: +Notes: - - Genome coordinates and reference allele will be updated to target assembly. - - Reference genome is genome sequence of target assembly. - - If the reference genome sequence file (../database/genome/hg18.fa) was - not indexed, CrossMap will automatically indexed it (only the first time - you run CrossMap). - - In the output VCF file, whether the chromosome IDs contain “chr” or not - depends on the format of the input VCF file. +- Genome coordinates and reference allele will be updated to target assembly. +- Reference genome is genome sequence of target assembly. +- If the reference genome sequence file (../database/genome/hg18.fa) was + not indexed, CrossMap will automatically indexed it (only the first time + you run CrossMap). +- In the output VCF file, whether the chromosome IDs contain “chr” or not + depends on the format of the input VCF file. -Please see `the manual `__ for more details -]]> + ]]> 10.1093/bioinformatics/btt730 diff -r af9e03d85771 -r 37c8b1afc814 macros.xml --- a/macros.xml Tue Sep 26 04:47:28 2017 -0400 +++ b/macros.xml Thu Oct 19 12:40:03 2017 -0400 @@ -2,12 +2,11 @@ - ucsc-wigtobigwig - crossmap + crossmap - 0.2.2 + 0.2.5 @@ -16,7 +15,9 @@ - CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' + &1 | head -n 1 | grep -E --only-matching 'CrossMap.*' + ]]> @@ -26,25 +27,18 @@ - - - - + + - + - - - - - - CrossMap -------- diff -r af9e03d85771 -r 37c8b1afc814 test-data/cached_locally/aToB.over.chain --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/aToB.over.chain Thu Oct 19 12:40:03 2017 -0400 @@ -0,0 +1,498 @@ +chain 21270171362 chr1 249250621 + 10000 249233096 chr1 247249719 + 0 247199719 2 +619 137 0 +166661 50000 50000 +40302 50000 50000 +153649 50000 50000 +1098479 1 1 +47 1 1 +73 117 114 +773 1 1 +43 1 1 +864369 2 2 +51 3 0 +104 13694 13694 +104 0 3 +51 2 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The liftOver.loc file has this format (white space +#characters are TAB characters): +# +# +# +#So, for example, if you had the chain file to convert from anoCar1 to galGal3 +#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, +#then the liftOver.loc entry would look like this: +# +# +# +# +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +# +#and your /depot/data2/galaxy/anoCar1/liftOver directory would +#contain all of your "chain" files (e.g.): +# +#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain +#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain +#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain +#...etc... +# +#Your liftOver.loc file should include an entry per line for each build you can +#convert. For example: +# +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +#anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain +#anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain +#...etc... + +A B ${__HERE__}/aToB.over.chain diff -r af9e03d85771 -r 37c8b1afc814 test-data/test_bam_01_output_a.bam Binary file test-data/test_bam_01_output_a.bam has changed diff -r af9e03d85771 -r 37c8b1afc814 test-data/test_bam_01_output_a.unmap.bam Binary file test-data/test_bam_01_output_a.unmap.bam has changed diff -r af9e03d85771 -r 37c8b1afc814 test-data/test_bed_01_output_a__only_fails.bed diff -r af9e03d85771 -r 37c8b1afc814 test-data/test_bed_02_output_a__only_fails.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_02_output_a__only_fails.bed Thu Oct 19 12:40:03 2017 -0400 @@ -0,0 +1,5 @@ +chr1 100 10000 +chr2 100 10000 +chr3 100 10000 +chr4 8941700 8947200 +chr5 1 100000000 diff -r af9e03d85771 -r 37c8b1afc814 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Oct 19 12:40:03 2017 -0400 @@ -0,0 +1,12 @@ + + + + value, dbkey, name, path + +
+ + + dbkey, name, value + +
+