# HG changeset patch # User iuc # Date 1508482275 14400 # Node ID a40d9af7d058beff8233769c54d7d042a571791e # Parent 734eedede47ce1a54409052b4afc9cfd5a7eceb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5 diff -r 734eedede47c -r a40d9af7d058 crossmap_vcf.xml --- a/crossmap_vcf.xml Tue Sep 26 05:45:41 2017 -0400 +++ b/crossmap_vcf.xml Fri Oct 20 02:51:15 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 734eedede47c -r a40d9af7d058 dump2/.gitignore --- a/dump2/.gitignore Tue Sep 26 05:45:41 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -* diff -r 734eedede47c -r a40d9af7d058 dump2/out.bam.bam diff -r 734eedede47c -r a40d9af7d058 dump2/out.bam.unmap.bam diff -r 734eedede47c -r a40d9af7d058 dump2/out2.bam Binary file dump2/out2.bam has changed diff -r 734eedede47c -r a40d9af7d058 dump2/out2.sorted.bam Binary file dump2/out2.sorted.bam has changed diff -r 734eedede47c -r a40d9af7d058 dump2/out2.sorted.bam.bai Binary file dump2/out2.sorted.bam.bai has changed diff -r 734eedede47c -r a40d9af7d058 dump2/out2.sorted.bam.bam Binary file dump2/out2.sorted.bam.bam has changed diff -r 734eedede47c -r a40d9af7d058 dump2/output2.bam diff -r 734eedede47c -r a40d9af7d058 dump2/output2.unmap.bam diff -r 734eedede47c -r a40d9af7d058 macros.xml --- a/macros.xml Tue Sep 26 05:45:41 2017 -0400 +++ b/macros.xml Fri Oct 20 02:51:15 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 734eedede47c -r a40d9af7d058 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 Fri Oct 20 02:51:15 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 2 +134936 50000 50000 +1161048 150000 60000 +1440092 27273 50000 +7590365 50000 50000 +116914 100000 50000 +237250 50000 50000 +3518496 50000 50000 +12702424 150000 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3 +221 17 17 +1525 8 0 +413 1 1 +32 2 2 +1573 12 12 +2258676 + +chain 18404394637 chr3 198022430 + 60000 197962430 chr3 199501827 + 35000 199446827 3 +13552792 0 1 +585083 0 1 +2092 1 2 +71 0 1 +31067262 0 1 +90 1 0 +5628461 0 15 +788 1 0 +3676 0 2 +35 1 1 +4682 1 0 +1295 0 5 +437 53 42 +326 0 2 +3309 1 1 +40 1 1 +998 0 3 +3584 5 0 +930 5 7 +845 1 1 +28 2 1 +303 0 1 +507 0 5 +5088 1 0 +2185 10046 10048 +949 4 4 +35 1 1 +2874 0 1 +6717 0 1 +2823 1 0 +703 0 4 +5143 1 0 +2490 10 10 +162 7 7 +6308 0 15 +15177535 152352 260003 +2532 1 0 +1633 2 2 +24207544 3000000 4400000 +60453436 0 4 +40076813 20999 20000 +8195 1 1 +44 1 1 +1408 1 1 +33 1 1 +172 3 4 +25 1 1 +538 13 13 +173 1 1 +27 1 1 +636 1 1 +28 1 1 +470 3 3 +112 1 1 +375 1 1 +26 26 0 +115 78 0 +52 23 0 +104 26 0 +15 231 0 +56 1 1 +20 1 1 +815 16 16 +484 1 1 +49 18 0 +509 4 3 +23 1 1 +391 1 1 +44 1 1 +1278 0 4 +32 1 1 +263 4 0 +27 1 1 +2416 0 2 +3184 43 43 +1150 13 13 +736 1 1 +47 1 1 +1416 1 1 +20 1 1 +1020 1 1 +25 1 1 +482 5 0 +716 1 0 +1697 1 1 +29 1 1 +1270261 23108 27000 +40930 1 0 +17455 1 1 +28 4 4 +43 0 491 +1679 1 1 +33 7 5 +29 1 3 +54863 53 16 +7653 2 2 +29 2 2 +15 0 30 +180 0 75 +215 45 0 +360 915 0 +6188 96 0 +17 288 0 +1388 1 1 +37 1 1 +7956 0 1 +374 0 1 +2442058 + +chain 310844 chr4 191154276 + 9241835 9252105 chr4 191273063 + 8941714 8947231 850 +2726 14 14 +243 9 9 +78 4 4 +157 213 211 +265 85 85 +524 4751 0 +379 283 283 +539 + +chain 9105 chr4 191154276 + 8982741 8983189 chr10 135374737 - 120304868 120305301 22041837 +59 380 365 +9 diff -r 734eedede47c -r a40d9af7d058 test-data/cached_locally/liftOver.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/liftOver.loc Fri Oct 20 02:51:15 2017 -0400 @@ -0,0 +1,32 @@ +#This is a sample file distributed with Galaxy that is used by the +#liftOver tools. 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 734eedede47c -r a40d9af7d058 test-data/test_bam_01_output_a.bam Binary file test-data/test_bam_01_output_a.bam has changed diff -r 734eedede47c -r a40d9af7d058 test-data/test_bam_01_output_a.unmap.bam Binary file test-data/test_bam_01_output_a.unmap.bam has changed diff -r 734eedede47c -r a40d9af7d058 test-data/test_bed_01_output_a__only_fails.bed diff -r 734eedede47c -r a40d9af7d058 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 Fri Oct 20 02:51:15 2017 -0400 @@ -0,0 +1,5 @@ +chr1 100 10000 +chr2 100 10000 +chr3 100 10000 +chr4 8941700 8947200 +chr5 1 100000000 diff -r 734eedede47c -r a40d9af7d058 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Oct 20 02:51:15 2017 -0400 @@ -0,0 +1,12 @@ + + + + value, dbkey, name, path + +
+ + + dbkey, name, value + +
+