# HG changeset patch # User iuc # Date 1508482241 14400 # Node ID 3b82b6febfd322614c4eb4ced945fb53fdcd6bd9 # Parent 143ec4d1c8f325c1418ad66c0885ab9c41d4f050 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5 diff -r 143ec4d1c8f3 -r 3b82b6febfd3 crossmap_bigwig.xml --- a/crossmap_bigwig.xml Tue Sep 26 05:45:25 2017 -0400 +++ b/crossmap_bigwig.xml Fri Oct 20 02:50:41 2017 -0400 @@ -8,47 +8,35 @@ - - - - - - - - - - - - + + - + - - + + + + + + - - + @@ -59,16 +47,15 @@ BigWig ------ - Input wiggle data can be in variableStep (for data with irregular - intervals) or fixedStep (for data with regular intervals). Regardless of - the input, the output will always in bedGraph format. bedGraph format is - similar to wiggle format and can be converted into BigWig format using UCSC - wigToBigWig tool. We export files in bedGraph because it is usually much - smaller than file in wiggle format, and more importantly, CrossMap - internally transforms wiggle into bedGraph to increase running speed. +Input wiggle data can be in variableStep (for data with irregular +intervals) or fixedStep (for data with regular intervals). Regardless of +the input, the output will always in bedGraph format. bedGraph format is +similar to wiggle format and can be converted into BigWig format using UCSC +wigToBigWig tool. We export files in bedGraph because it is usually much +smaller than file in wiggle format, and more importantly, CrossMap +internally transforms wiggle into bedGraph to increase running speed. -Please see `the manual `__ for more details -]]> + ]]> 10.1093/bioinformatics/btt730 diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/.gitignore --- a/dump2/.gitignore Tue Sep 26 05:45:25 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -* diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/out.bam.bam diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/out.bam.unmap.bam diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/out2.bam Binary file dump2/out2.bam has changed diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/out2.sorted.bam Binary file dump2/out2.sorted.bam has changed diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/out2.sorted.bam.bai Binary file dump2/out2.sorted.bam.bai has changed diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/out2.sorted.bam.bam Binary file dump2/out2.sorted.bam.bam has changed diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/output2.bam diff -r 143ec4d1c8f3 -r 3b82b6febfd3 dump2/output2.unmap.bam diff -r 143ec4d1c8f3 -r 3b82b6febfd3 macros.xml --- a/macros.xml Tue Sep 26 05:45:25 2017 -0400 +++ b/macros.xml Fri Oct 20 02:50:41 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 143ec4d1c8f3 -r 3b82b6febfd3 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 02:50:41 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 +5615 1 1 +37 1 1 +3172 6 4 +190 1 1 +34 1 1 +380 0 1 +2099 3 0 +765 2 2 +366 0 4 +1186 1 0 +460 0 1 +1242 28 28 +574 1 1 +21 1 1 +1460 1 1 +105 1 1 +701 3 0 +239 0 1 +970 11 11 +2365 1 1 +21 1 1 +384 8 8 +996 2 0 +10383 2 0 +713 0 1 +5188 1 1 +30 1 1 +1233 1 0 +132 1 1 +44 1 1 +1123 22 22 +1810 1 0 +512 1 1 +39 1 1 +1096 0 16 +743 1 0 +9028 0 1 +2506 0 6 +8446 2 0 +5505 0 3 +7541 1 0 +109864 50000 50000 +78698 50000 50000 +127263 50000 50000 +170669 50000 50000 +38311 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161 0 +13 66 0 +12 71 1 +12548 30000 30000 +952154 41011 25000 +1914 1 0 +225 1 1 +57 1 1 +2910 0 1 +471 1 0 +1956 1 1 +43 1 1 +991 0 92 +2863 3 0 +1838 306 0 +1006 30 0 +206 1 1 +27 0 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 143ec4d1c8f3 -r 3b82b6febfd3 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 02:50:41 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 143ec4d1c8f3 -r 3b82b6febfd3 test-data/test_bam_01_output_a.bam Binary file test-data/test_bam_01_output_a.bam has changed diff -r 143ec4d1c8f3 -r 3b82b6febfd3 test-data/test_bam_01_output_a.unmap.bam Binary file test-data/test_bam_01_output_a.unmap.bam has changed diff -r 143ec4d1c8f3 -r 3b82b6febfd3 test-data/test_bed_01_output_a__only_fails.bed diff -r 143ec4d1c8f3 -r 3b82b6febfd3 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 02:50:41 2017 -0400 @@ -0,0 +1,5 @@ +chr1 100 10000 +chr2 100 10000 +chr3 100 10000 +chr4 8941700 8947200 +chr5 1 100000000 diff -r 143ec4d1c8f3 -r 3b82b6febfd3 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 02:50:41 2017 -0400 @@ -0,0 +1,12 @@ + + + + value, dbkey, name, path + +
+ + + dbkey, name, value + +
+