# HG changeset patch # User bgruening # Date 1487043841 18000 # Node ID f112bf3dd5ffbc9b3cd06c0593b78fa4703e37a2 # Parent cda51d96a9bcb8e87632b03a6ba67f7fa1311547 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 diff -r cda51d96a9bc -r f112bf3dd5ff MethylDackel.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MethylDackel.xml Mon Feb 13 22:44:01 2017 -0500 @@ -0,0 +1,453 @@ + + A tool for processing bisulfite sequencing alignments + + methyldackel + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + main_task['task'] == "extract" + not advanced_options['logit'] + not advanced_options['methylKit'] + not advanced_options['counts'] + not advanced_options['fraction'] + + + main_task['task'] == "extract" and advanced_options['logit'] + + + main_task['task'] == "extract" and advanced_options['methylKit'] + + + main_task['task'] == "extract" and advanced_options['counts'] + + + main_task['task'] == "extract" and advanced_options['fraction'] + + + main_task['task'] == 'extract' + advanced_options['options'] == "yes" + advanced_options['CHG'] + not advanced_options['logit'] + not advanced_options['methylKit'] + not advanced_options['counts'] + not advanced_options['fraction'] + + + main_task['task'] == "extract" and advanced_options['logit'] + advanced_options['options'] == "yes" + advanced_options['CHG'] + + + main_task['task'] == "extract" and advanced_options['methylKit'] + advanced_options['options'] == "yes" + advanced_options['CHG'] + + + main_task['task'] == "extract" and advanced_options['counts'] + advanced_options['options'] == "yes" + advanced_options['CHG'] + + + main_task['task'] == "extract" and advanced_options['fraction'] + advanced_options['options'] == "yes" + advanced_options['CHG'] + + + main_task['task'] == 'extract' + advanced_options['options'] == "yes" + advanced_options['CHH'] + not advanced_options['logit'] + not advanced_options['methylKit'] + not advanced_options['counts'] + not advanced_options['fraction'] + + + main_task['task'] == "extract" and advanced_options['logit'] + advanced_options['options'] == "yes" + advanced_options['CHH'] + + + main_task['task'] == "extract" and advanced_options['methylKit'] + advanced_options['options'] == "yes" + advanced_options['CHH'] + + + main_task['task'] == "extract" and advanced_options['counts'] + advanced_options['options'] == "yes" + advanced_options['CHH'] + + + main_task['task'] == "extract" and advanced_options['fraction'] + advanced_options['options'] == "yes" + advanced_options['CHH'] + + + main_task['task'] == 'mbias' + + + main_task['task'] == 'mbias' + + + main_task['task'] == 'mbias' + + + main_task['task'] == 'mbias' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r cda51d96a9bc -r f112bf3dd5ff PileOMeth.xml --- a/PileOMeth.xml Mon Feb 13 07:09:59 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,289 +0,0 @@ - - A tool for processing bisulfite sequencing alignments - - pileometh - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - main_task['task'] == "extract" - - - main_task['task'] == 'extract' - advanced_options['options'] == "yes" - advanced_options['CHG'] - - - main_task['task'] == 'extract' - advanced_options['options'] == "yes" - advanced_options['CHH'] - - - main_task['task'] == 'mbias' - - - main_task['task'] == 'mbias' - - - main_task['task'] == 'mbias' - - - main_task['task'] == 'mbias' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r cda51d96a9bc -r f112bf3dd5ff test-data/test_3.bedGraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3.bedGraph Mon Feb 13 22:44:01 2017 -0500 @@ -0,0 +1,49 @@ +track type="bedGraph" description="output CpG methylation fractions" +chrCG 0 1 1.000000 +chrCG 2 3 1.000000 +chrCG 4 5 1.000000 +chrCG 6 7 1.000000 +chrCG 8 9 1.000000 +chrCG 10 11 1.000000 +chrCG 12 13 1.000000 +chrCG 14 15 1.000000 +chrCG 18 19 1.000000 +chrCG 20 21 1.000000 +chrCG 22 23 1.000000 +chrCG 24 25 1.000000 +chrCG 26 27 1.000000 +chrCG 28 29 1.000000 +chrCG 30 31 1.000000 +chrCG 32 33 1.000000 +chrCG 34 35 1.000000 +chrCG 36 37 1.000000 +chrCG 38 39 1.000000 +chrCG 40 41 1.000000 +chrCG 42 43 1.000000 +chrCG 44 45 1.000000 +chrCG 46 47 1.000000 +chrCG 48 49 1.000000 +chrCG 50 51 1.000000 +chrCG 52 53 1.000000 +chrCG 54 55 1.000000 +chrCG 56 57 1.000000 +chrCG 58 59 1.000000 +chrCG 60 61 1.000000 +chrCG 62 63 1.000000 +chrCG 64 65 1.000000 +chrCG 66 67 1.000000 +chrCG 68 69 1.000000 +chrCG 70 71 1.000000 +chrCG 72 73 1.000000 +chrCG 74 75 1.000000 +chrCG 76 77 1.000000 +chrCG 78 79 1.000000 +chrCG 80 81 1.000000 +chrCG 82 83 1.000000 +chrCG 84 85 1.000000 +chrCG 86 87 1.000000 +chrCG 88 89 1.000000 +chrCG 90 91 1.000000 +chrCG 92 93 1.000000 +chrCG 94 95 1.000000 +chrCG 96 97 1.000000 diff -r cda51d96a9bc -r f112bf3dd5ff test-data/test_4.bedGraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_4.bedGraph Mon Feb 13 22:44:01 2017 -0500 @@ -0,0 +1,49 @@ +track type="bedGraph" description="output CpG logit transformed methylation fractions" +chrCG 0 1 inf +chrCG 2 3 inf +chrCG 4 5 inf +chrCG 6 7 inf +chrCG 8 9 inf +chrCG 10 11 inf +chrCG 12 13 inf +chrCG 14 15 inf +chrCG 18 19 inf +chrCG 20 21 inf +chrCG 22 23 inf +chrCG 24 25 inf +chrCG 26 27 inf +chrCG 28 29 inf +chrCG 30 31 inf +chrCG 32 33 inf +chrCG 34 35 inf +chrCG 36 37 inf +chrCG 38 39 inf +chrCG 40 41 inf +chrCG 42 43 inf +chrCG 44 45 inf +chrCG 46 47 inf +chrCG 48 49 inf +chrCG 50 51 inf +chrCG 52 53 inf +chrCG 54 55 inf +chrCG 56 57 inf +chrCG 58 59 inf +chrCG 60 61 inf +chrCG 62 63 inf +chrCG 64 65 inf +chrCG 66 67 inf +chrCG 68 69 inf +chrCG 70 71 inf +chrCG 72 73 inf +chrCG 74 75 inf +chrCG 76 77 inf +chrCG 78 79 inf +chrCG 80 81 inf +chrCG 82 83 inf +chrCG 84 85 inf +chrCG 86 87 inf +chrCG 88 89 inf +chrCG 90 91 inf +chrCG 92 93 inf +chrCG 94 95 inf +chrCG 96 97 inf diff -r cda51d96a9bc -r f112bf3dd5ff test-data/test_5.methylKit --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_5.methylKit Mon Feb 13 22:44:01 2017 -0500 @@ -0,0 +1,49 @@ +chrBase chr base strand coverage freqC freqT +chrCG.1 chrCG 1 F 1 100.00 0.00 +chrCG.3 chrCG 3 F 1 100.00 0.00 +chrCG.5 chrCG 5 F 1 100.00 0.00 +chrCG.7 chrCG 7 F 1 100.00 0.00 +chrCG.9 chrCG 9 F 1 100.00 0.00 +chrCG.11 chrCG 11 F 1 100.00 0.00 +chrCG.13 chrCG 13 F 1 100.00 0.00 +chrCG.15 chrCG 15 F 1 100.00 0.00 +chrCG.19 chrCG 19 F 1 100.00 0.00 +chrCG.21 chrCG 21 F 1 100.00 0.00 +chrCG.23 chrCG 23 F 1 100.00 0.00 +chrCG.25 chrCG 25 F 1 100.00 0.00 +chrCG.27 chrCG 27 F 1 100.00 0.00 +chrCG.29 chrCG 29 F 1 100.00 0.00 +chrCG.31 chrCG 31 F 1 100.00 0.00 +chrCG.33 chrCG 33 F 1 100.00 0.00 +chrCG.35 chrCG 35 F 1 100.00 0.00 +chrCG.37 chrCG 37 F 1 100.00 0.00 +chrCG.39 chrCG 39 F 1 100.00 0.00 +chrCG.41 chrCG 41 F 1 100.00 0.00 +chrCG.43 chrCG 43 F 1 100.00 0.00 +chrCG.45 chrCG 45 F 1 100.00 0.00 +chrCG.47 chrCG 47 F 1 100.00 0.00 +chrCG.49 chrCG 49 F 1 100.00 0.00 +chrCG.51 chrCG 51 F 1 100.00 0.00 +chrCG.53 chrCG 53 F 1 100.00 0.00 +chrCG.55 chrCG 55 F 1 100.00 0.00 +chrCG.57 chrCG 57 F 1 100.00 0.00 +chrCG.59 chrCG 59 F 1 100.00 0.00 +chrCG.61 chrCG 61 F 1 100.00 0.00 +chrCG.63 chrCG 63 F 1 100.00 0.00 +chrCG.65 chrCG 65 F 1 100.00 0.00 +chrCG.67 chrCG 67 F 1 100.00 0.00 +chrCG.69 chrCG 69 F 1 100.00 0.00 +chrCG.71 chrCG 71 F 1 100.00 0.00 +chrCG.73 chrCG 73 F 1 100.00 0.00 +chrCG.75 chrCG 75 F 1 100.00 0.00 +chrCG.77 chrCG 77 F 1 100.00 0.00 +chrCG.79 chrCG 79 F 1 100.00 0.00 +chrCG.81 chrCG 81 F 1 100.00 0.00 +chrCG.83 chrCG 83 F 1 100.00 0.00 +chrCG.85 chrCG 85 F 1 100.00 0.00 +chrCG.87 chrCG 87 F 1 100.00 0.00 +chrCG.89 chrCG 89 F 1 100.00 0.00 +chrCG.91 chrCG 91 F 1 100.00 0.00 +chrCG.93 chrCG 93 F 1 100.00 0.00 +chrCG.95 chrCG 95 F 1 100.00 0.00 +chrCG.97 chrCG 97 F 1 100.00 0.00 diff -r cda51d96a9bc -r f112bf3dd5ff tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 13 07:09:59 2017 -0500 +++ b/tool_dependencies.xml Mon Feb 13 22:44:01 2017 -0500 @@ -1,21 +1,21 @@ - + - https://github.com/dpryan79/PileOMeth/archive/0.1.13.tar.gz + https://github.com/dpryan79/MethylDackel/archive/0.2.1.tar.gz make make install prefix=$INSTALL_DIR/bin $INSTALL_DIR/bin - $INSTALL_DIR + $INSTALL_DIR