# HG changeset patch # User bgruening # Date 1442590795 14400 # Node ID 65575e70af7e88b1564eafd4e305a747ee2bdb90 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 033c712216994524fdd120b771052ac4ca9e51c0-dirty diff -r 000000000000 -r 65575e70af7e PileOMeth.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PileOMeth.xml Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,212 @@ + + A tool for processing bisulfite sequencing alignments + + pileometh + + + + + + + + + + &1 | head -n 2 | tail -n 1]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + main_task['task'] == "extract" + + + main_task['task'] == 'extract' + advanced_options['options'] == "yes" + advanced_options['CHG'] == "--CHG" + + + main_task['task'] == 'extract' + advanced_options['options'] == "yes" + advanced_options['CHH'] == "--CHH" + + + main_task['task'] == 'mbias' + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 65575e70af7e all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# diff -r 000000000000 -r 65575e70af7e static/images/example.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/example.svg Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,653 @@ + +Original Top Strand + +Original Top Strand + + +CpG Methylation % +Position along mapped read (5'->3' of + strand) + +0 + + +25 + + +50 + + +75 + + +100 + +0.00 + +0.05 + +0.10 + +0.15 + +0.20 + +0.25 + +0.30 + +0.35 + + + + +--OT 2,0,0,98 + + + +#1 + +#2 + diff -r 000000000000 -r 65575e70af7e test-data/cg100.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cg100.fa Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,2 @@ +>chrCG +cgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcA diff -r 000000000000 -r 65575e70af7e test-data/cg_aln.bam Binary file test-data/cg_aln.bam has changed diff -r 000000000000 -r 65575e70af7e test-data/test_1.bedGraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1.bedGraph Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,49 @@ +track type="bedGraph" description="output CpG methylation levels" +chrCG 0 1 100 1 0 +chrCG 2 3 100 1 0 +chrCG 4 5 100 1 0 +chrCG 6 7 100 1 0 +chrCG 8 9 100 1 0 +chrCG 10 11 100 1 0 +chrCG 12 13 100 1 0 +chrCG 14 15 100 1 0 +chrCG 18 19 100 1 0 +chrCG 20 21 100 1 0 +chrCG 22 23 100 1 0 +chrCG 24 25 100 1 0 +chrCG 26 27 100 1 0 +chrCG 28 29 100 1 0 +chrCG 30 31 100 1 0 +chrCG 32 33 100 1 0 +chrCG 34 35 100 1 0 +chrCG 36 37 100 1 0 +chrCG 38 39 100 1 0 +chrCG 40 41 100 1 0 +chrCG 42 43 100 1 0 +chrCG 44 45 100 1 0 +chrCG 46 47 100 1 0 +chrCG 48 49 100 1 0 +chrCG 50 51 100 1 0 +chrCG 52 53 100 1 0 +chrCG 54 55 100 1 0 +chrCG 56 57 100 1 0 +chrCG 58 59 100 1 0 +chrCG 60 61 100 1 0 +chrCG 62 63 100 1 0 +chrCG 64 65 100 1 0 +chrCG 66 67 100 1 0 +chrCG 68 69 100 1 0 +chrCG 70 71 100 1 0 +chrCG 72 73 100 1 0 +chrCG 74 75 100 1 0 +chrCG 76 77 100 1 0 +chrCG 78 79 100 1 0 +chrCG 80 81 100 1 0 +chrCG 82 83 100 1 0 +chrCG 84 85 100 1 0 +chrCG 86 87 100 1 0 +chrCG 88 89 100 1 0 +chrCG 90 91 100 1 0 +chrCG 92 93 100 1 0 +chrCG 94 95 100 1 0 +chrCG 96 97 100 1 0 diff -r 000000000000 -r 65575e70af7e test-data/test_2_output.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_output.svg Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,390 @@ + +Original Top Strand + +Original Top Strand + + +CpG Methylation % +Position along mapped read (5'->3' of + strand) + +0 + + +10 + + +20 + + +30 + + +40 + + +50 + + +60 + + +70 + + +80 + + +90 + + +100 + +0.00 + +0.05 + +0.10 + +0.15 + +0.20 + +0.25 + +0.30 + +0.35 + +0.40 + +0.45 + +0.50 + +0.55 + +0.60 + +0.65 + +0.70 + +0.75 + +0.80 + +0.85 + +0.90 + +0.95 + +1.00 + + + + +--OT 18,0,0,0 + + +#1 + +#2 + diff -r 000000000000 -r 65575e70af7e tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# diff -r 000000000000 -r 65575e70af7e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff -r 000000000000 -r 65575e70af7e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Sep 18 11:39:55 2015 -0400 @@ -0,0 +1,22 @@ + + + + + + https://github.com/dpryan79/PileOMeth/archive/0.1.5.tar.gz + make + make install prefix=$INSTALL_DIR + + $INSTALL_DIR + $INSTALL_DIR + + + + + + + +