# HG changeset patch # User iuc # Date 1508482104 14400 # Node ID 79f9e32b380b657a6a68679e24698243d8626e69 # Parent 1e881a00d8ff799728641bcd6e2223aec6d3cc03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5 diff -r 1e881a00d8ff -r 79f9e32b380b crossmap_bed.xml --- a/crossmap_bed.xml Tue Sep 26 06:05:09 2017 -0400 +++ b/crossmap_bed.xml Fri Oct 20 02:48:24 2017 -0400 @@ -7,84 +7,96 @@ - out.bed +stdout/out.bed: valid and invalid combined - '${input_file}' +2. CrossMap bed x.chain in.bed out.bed +out.bed: valid only +out.bed.unmap: invalid only +--> + - #end if +'${input}' - '${output}' +#if $merge_unmapped_entries: + > '${output_combined}' +#else: + '${output_valid}' + && mv '${output_valid}.unmap' '${output_failed}' +#end if + ]]> - - + - - - - - - - - - - - + - - + + merge_unmapped_entries is False + + + merge_unmapped_entries is False + + + + merge_unmapped_entries is True + - - + + - - + - + + - + + - - + + + + - - - + + - - + - + + - - + + - + + + + - + + + + + + + `__ for more details. -]]> + ]]> 10.1093/bioinformatics/btt730 diff -r 1e881a00d8ff -r 79f9e32b380b macros.xml --- a/macros.xml Tue Sep 26 06:05:09 2017 -0400 +++ b/macros.xml Fri Oct 20 02:48:24 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 1e881a00d8ff -r 79f9e32b380b 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 02:48:24 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 50000 +16145012 0 1 +7772 1 0 +4705841 0 1 +52977198 50000 50000 +157344 21065 50000 +16604841 50000 50000 +189539 150000 50000 +398739 21050000 20290000 +195588 50000 50000 +186739 150000 50000 +175055 50000 50000 +201709 100000 50000 +126477 130183 50000 +381 0 3 +315 0 2 +62 1 1 +45 1 0 +19 0 1 +8 1 1 +1158 1 0 +314 12 13 +2849 3 0 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+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 1e881a00d8ff -r 79f9e32b380b 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 02:48:24 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 1e881a00d8ff -r 79f9e32b380b test-data/test_bam_01_output_a.bam Binary file test-data/test_bam_01_output_a.bam has changed diff -r 1e881a00d8ff -r 79f9e32b380b test-data/test_bam_01_output_a.unmap.bam Binary file test-data/test_bam_01_output_a.unmap.bam has changed diff -r 1e881a00d8ff -r 79f9e32b380b test-data/test_bed_01_output_a__only_fails.bed diff -r 1e881a00d8ff -r 79f9e32b380b 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 02:48:24 2017 -0400 @@ -0,0 +1,5 @@ +chr1 100 10000 +chr2 100 10000 +chr3 100 10000 +chr4 8941700 8947200 +chr5 1 100000000 diff -r 1e881a00d8ff -r 79f9e32b380b 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 02:48:24 2017 -0400 @@ -0,0 +1,12 @@ + + + + value, dbkey, name, path + +
+ + + dbkey, name, value + +
+