| Previous changeset 8:183cb55b1729 (2018-08-24) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit c1027a3f78bca2fd8a53f076ef718ea5adbf4a8a" |
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modified:
MethylDackel.xml |
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added:
macros.xml test-data/mappability.bigwig |
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removed:
static/images/example.svg test-data/test7_output.tsv test-data/test8_output.tsv test-data/test_1.bedGraph test-data/test_2.bedGraph test-data/test_2_output.svg test-data/test_3.bedGraph test-data/test_4.bedGraph test-data/test_5.methylKit |
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| diff -r 183cb55b1729 -r d6787bab7b11 MethylDackel.xml --- a/MethylDackel.xml Fri Aug 24 17:15:24 2018 -0400 +++ b/MethylDackel.xml Sat Jun 05 09:18:31 2021 +0000 |
| [ |
| b'@@ -1,8 +1,10 @@\n-<tool id="pileometh" name="MethylDackel" version="0.3.0.1">\n+<tool id="pileometh" name="MethylDackel" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">\n <description>A tool for processing bisulfite sequencing alignments</description>\n- <requirements>\n- <requirement type="package" version="0.3.0">methyldackel</requirement>\n- </requirements>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="requirements"/>\n <version_command><![CDATA[MethylDackel --version]]></version_command>\n <command detect_errors="aggressive"><![CDATA[\n #if $reference_source.reference_source_selector == "cached":\n@@ -11,73 +13,80 @@\n ln -s $reference_source.ref_file reference.fasta &&\n #end if\n \n+ ln -s \'$input_sortedAlignBAM\' ./infile.bam &&\n+ ln -s \'${input_sortedAlignBAM.metadata.bam_index}\' infile.bai &&\n+\n MethylDackel\n $main_task.task\n \n -@ \\${GALAXY_SLOTS:-4}\n- #if $main_task.task == "extract":\n+ #if $main_task.task == \'extract\':\n -o output\n $main_task.mergeContext\n- #if str($main_task.OT).strip() != "":\n+ #if str($main_task.OT).strip() != \'\':\n --OT $main_task.OT\n #end if\n- #if str($main_task.OB).strip() != "":\n+ #if str($main_task.OB).strip() != \'\':\n --OB $main_task.OB\n #end if\n- #if str($main_task.CTOT).strip() != "":\n+ #if str($main_task.CTOT).strip() != \'\':\n --CTOT $main_task.CTOT\n #end if\n- #if str($main_task.CTOB).strip() != "":\n+ #if str($main_task.CTOB).strip() != \'\':\n --CTOB $main_task.CTOB\n #end if\n+ #if str($main_task.mappability_options.mappability_status) == \'True\':\n+ -M \'${main_task.mappability_options.mappability}\'\n+ --mappabilityThreshold $main_task.mappability_options.mappabilityThreshold\n+ --minMappableBases $main_task.mappability_options.minMappableBases \n+ #end if\n+ #end if\n+ #if $advanced_options.mbias_regionString:\n+ -r $advanced_options.mbias_regionString\n+ #end if\n+ #if $regionBed_options.regionBed_status == \'True\':\n+ -l \'$regionBed_options.regionBed\'\n+ $regionBed_options.keepStrand\n+ #end if\n+ $advanced_options.keepDupes\n+ $advanced_options.keepSingleton\n+ $advanced_options.keepDiscordant\n+ -q $advanced_options.min_mapq\n+ -p $advanced_options.min_phred\n+ #if $advanced_options.methylation_metrics\n+ #for $context_methylation in $advanced_options.methylation_metrics:\n+ $context_methylation\n+ #end for\n+ #end if\n+ #if $main_task.task == \'extract\':\n+ --minOppositeDepth $advanced_options.minOppositeDepth\n+ --maxVariantFrac $advanced_options.maxVariantFrac\n+ -d $advanced_options.min_pbdepth\n+ --ignoreFlags $advanced_options.ignoreFlags\n+ --requireFlags $advanced_options.requireFlags\n+ #if $main_task.extract_outputs\n+ $main_task.extract_outputs\n+ #end if\n+ #if str($advanced_options.nOT).strip() != \'\':\n+ --nOT $advanced_options.nOT\n+ #end if\n+ #if str($advanced_options.nOB).strip() != \'\':\n+ --nOB $advanced_options.nOB\n+ #end if\n+ #if str($advanced_options.nCTOT).strip() != \'\':\n+ --nCTOT $advanced_options.nCTOT\n+ #end if\n+ '..b'ame="main_task">\n+ <param name="task" value="extract" />\n+ <conditional name="mappability_options">\n+ <param name="mappability_status" value="True"/>\n+ <param name="mappability" value="mappability.bigwig" ftype="bigwig"/>\n+ <param name="mappabilityThreshold" value="0.1"/>\n+ <param name="minMappableBases" value="15"/>\n+ </conditional>\n+ </conditional>\n+ <output name="outFileExtractCpG" ftype="bedgraph">\n+ <assert_contents>\n+ <has_size value="66"/>\n+ </assert_contents>\n+ </output> \n+ </test>\n+ <!-- Test cytosine report-->\n+ <test expect_num_outputs="1">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" value="cg100.fa" ftype="fasta" />\n+ <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>\n+ <conditional name="main_task">\n+ <param name="task" value="extract" />\n+ <param name="extract_outputs" value="--cytosine_report" />\n+ </conditional>\n+ <output name="outFileExtractCpG" ftype="txt">\n+ <assert_contents>\n+ <has_size value="2147"/>\n+ </assert_contents>\n+ </output> \n </test>\n </tests>\n <help><![CDATA[\n \n-.. image:: $PATH_TO_IMAGES/MethylDackelLogo.png\n- :align: left\n-\n **What it does**\n \n MethylDackel (formerly named PileOMeth, which was a temporary name derived due to it using a PILEup to extract METHylation metrics) will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.\n@@ -450,9 +645,7 @@\n In an ideal experiment, we expect that the probability of observing a methylated C is constant across the length of any given read. In practice, however, there are often increases/decreases in observed methylation rate at the ends of reads and/or more global changes. These are termed methylation bias and including such regions in the extracted methylation metrics will result in noisier and less accurate data. For this reason, users are strongly encouraged to make a methylation bias plot.\n \n That command will create a methylation bias (mbias for short) plot for each of the strands for which there are valid alignments.\n-The resulting mbias graphs are in SVG format and can be viewed in most modern web browsers:\n-\n-.. image:: $PATH_TO_IMAGES/example.svg\n+The resulting mbias graphs are in SVG format and can be viewed in most modern web browsers.\n \n \n If you have paired-end data, both reads in the pair will be shown separately, as is the case above. The program will suggest regions for inclusion ("--OT 2,0,0,98" above) and mark them on the plot, if applicable. The format of this output is described in MethylDackel extract -h. These suggestions should not be accepted blindly; users are strongly encouraged to have a look for themselves and tweak the actual bounds as appropriate. The lines indicate the average methylation percentage at a given position and the shaded regions the 99.9% confidence interval around it. This is useful in gauging how many methylation calls a given position has relative to its neighbors. Note the spike in methylation at the end of read #2 and the corresponding dip at the beginning of read #1. This is common and these regions can be ignored with the suggested trimming bounds. Note also that the numbers refer to the first and last base that should be included during methylation extraction, not the last and first base to ignore!.\n@@ -490,6 +683,5 @@\n \n .. _MethylDackel: https://github.com/dpryan79/MethylDackel\n ]]></help>\n- <citations>\n- </citations>\n+ <expand macro="citations"/>\n </tool>\n' |
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| diff -r 183cb55b1729 -r d6787bab7b11 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jun 05 09:18:31 2021 +0000 |
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| @@ -0,0 +1,32 @@ +<macros> + <token name="@TOOL_VERSION@">0.5.2</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_3295</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3207</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">methyldackel</requirement> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{githubmethyldackel, + author = {Devon, Ryan}, + year = {2021}, + title = {MethylDackel}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/dpryan79/MethylDackel}, + } + </citation> + </citations> + </xml> +</macros> |
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| diff -r 183cb55b1729 -r d6787bab7b11 static/images/example.svg --- a/static/images/example.svg Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,653 +0,0 @@\n-<svg height="660" width="660"\n- xmlns="http://www.w3.org/2000/svg"\n- xmlns:xlink="http://www.w3.org/1999/xlink"\n- xmlns:ev="http://www.w3.org/2001/xml-events">\n-<title>Original Top Strand</title>\n-<rect x="0" y="0" width="660" height="660" fill="white" />\n-<text x="330" y="20" text-anchor="middle">Original Top Strand</text>\n-<line x1="80" y1="80" x2="80" y2="580" stroke="black" />\n-<line x1="80" y1="580" x2="580" y2="580" stroke="black" />\n-<text x="15" y="330" transform="rotate(270 15, 330)" text-anchor="middle" dominant-baseline="text-before-edge">CpG Methylation %</text>\n-<text x="330" y="620" text-anchor="middle">Position along mapped read (5\'->3\' of + strand)</text>\n-<line x1="80" y1="580" x2="80" y2="585" stroke="black" />\n-<text x="80" y="600" text-anchor="middle">0</text>\n-<line x1="205.000000" y1="80" x2="205.000000" y2="580" stroke-dasharray="5 5" stroke="grey" />\n-<line x1="205.000000" y1="580" x2="205.000000" y2="585" stroke="black" />\n-<text x="205.000000" y="600" text-anchor="middle">25</text>\n-<line x1="330.000000" y1="80" x2="330.000000" y2="580" stroke-dasharray="5 5" stroke="grey" />\n-<line x1="330.000000" y1="580" x2="330.000000" y2="585" stroke="black" />\n-<text x="330.000000" y="600" text-anchor="middle">50</text>\n-<line x1="455.000000" y1="80" x2="455.000000" y2="580" stroke-dasharray="5 5" stroke="grey" />\n-<line x1="455.000000" y1="580" x2="455.000000" y2="585" stroke="black" />\n-<text x="455.000000" y="600" text-anchor="middle">75</text>\n-<line x1="580.000000" y1="80" x2="580.000000" y2="580" stroke-dasharray="5 5" stroke="grey" />\n-<line x1="580.000000" y1="580" x2="580.000000" y2="585" stroke="black" />\n-<text x="580.000000" y="600" text-anchor="middle">100</text>\n-<line x1="80" y1="580.000000" x2="75" y2="580.000000" stroke="black" />\n-<text x="55" y="580.000000" text-anchor="middle" dominant-baseline="middle">0.00</text>\n-<line x1="80" y1="508.571429" x2="75" y2="508.571429" 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292.480033\n- L 515.000000 278.807781\n- L 520.000000 268.636213\n- L 525.000000 308.279329\n- L 530.000000 294.422028\n- L 535.000000 283.049759\n- L 540.000000 286.959707\n- L 545.000000 280.129386\n- L 550.000000 276.308186\n- L 555.000000 279.403227\n- L 560.000000 289.562109\n- L 565.000000 294.138363\n- L 570.000000 289.499051\n- L 575.000000 457.999187\n- L 580.000000 495.224302\n-" stroke="rgb(0,191,196)" stroke-width="2" fill-opacity="0"/>\n-<text x="650" y="650" text-anchor="end">--OT 2,0,0,98</text>\n-<line x1="90.000000" y1="580" x2="90.000000" y2="80" stroke-dasharray="5 1" stroke="rgb(248,118,109)" stroke-width="1" />\n-<line x1="570.000000" y1="580" x2="570.000000" y2="80" stroke-dasharray="5 1" stroke="rgb(0,191,196)" stroke-width="1" />\n-<rect x="590" y="310" width="20" height="20" fill="rgb(248,118,109)" />\n-<text x="615" y="320" text-anchor="start" dominant-baseline="middle">#1</text>\n-<rect x="590" y="330" width="20" height="20" fill="rgb(0,191,196)" />\n-<text x="615" y="340" text-anchor="start" dominant-baseline="middle">#2</text>\n-</svg>\n' |
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| diff -r 183cb55b1729 -r d6787bab7b11 test-data/mappability.bigwig |
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| Binary file test-data/mappability.bigwig has changed |
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| diff -r 183cb55b1729 -r d6787bab7b11 test-data/test7_output.tsv --- a/test-data/test7_output.tsv Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,99 +0,0 @@ -Strand Read Position nMethylated nUnmethylated -OT 1 1 1 0 -OT 2 1 1 0 -OT 1 3 1 0 -OT 2 3 1 0 -OT 1 5 1 0 -OT 2 5 1 0 -OT 1 7 1 0 -OT 2 7 1 0 -OT 1 9 1 0 -OT 2 9 1 0 -OT 1 11 1 0 -OT 2 11 1 0 -OT 1 13 1 0 -OT 2 13 1 0 -OT 1 15 1 0 -OT 2 15 1 0 -OT 1 17 0 1 -OT 2 17 1 0 -OT 1 19 1 0 -OT 2 19 1 0 -OT 1 21 1 0 -OT 2 21 1 0 -OT 1 23 1 0 -OT 2 23 1 0 -OT 1 25 1 0 -OT 2 25 1 0 -OT 1 27 1 0 -OT 2 27 1 0 -OT 1 29 1 0 -OT 2 29 1 0 -OT 1 31 1 0 -OT 2 31 1 0 -OT 1 33 1 0 -OT 2 33 1 0 -OT 1 35 1 0 -OT 2 35 1 0 -OT 1 37 1 0 -OT 2 37 1 0 -OT 1 39 1 0 -OT 2 39 1 0 -OT 1 41 1 0 -OT 2 41 1 0 -OT 1 43 1 0 -OT 2 43 1 0 -OT 1 45 1 0 -OT 2 45 1 0 -OT 1 47 1 0 -OT 2 47 1 0 -OT 1 49 1 0 -OT 2 49 1 0 -OT 1 51 1 0 -OT 2 51 1 0 -OT 1 53 1 0 -OT 2 53 1 0 -OT 1 55 1 0 -OT 2 55 1 0 -OT 1 57 1 0 -OT 2 57 1 0 -OT 1 59 1 0 -OT 2 59 1 0 -OT 1 61 1 0 -OT 2 61 1 0 -OT 1 63 1 0 -OT 2 63 1 0 -OT 1 65 1 0 -OT 2 65 1 0 -OT 1 67 1 0 -OT 2 67 1 0 -OT 1 69 1 0 -OT 2 69 1 0 -OT 1 71 1 0 -OT 2 71 1 0 -OT 1 73 1 0 -OT 2 73 1 0 -OT 1 75 1 0 -OT 2 75 1 0 -OT 1 77 1 0 -OT 2 77 1 0 -OT 1 79 1 0 -OT 2 79 1 0 -OT 1 81 1 0 -OT 2 81 1 0 -OT 1 83 1 0 -OT 2 83 1 0 -OT 1 85 1 0 -OT 2 85 1 0 -OT 1 87 1 0 -OT 2 87 1 0 -OT 1 89 1 0 -OT 2 89 1 0 -OT 1 91 1 0 -OT 2 91 1 0 -OT 1 93 1 0 -OT 2 93 1 0 -OT 1 95 1 0 -OT 2 95 1 0 -OT 1 97 1 0 -OT 2 97 1 0 |
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| diff -r 183cb55b1729 -r d6787bab7b11 test-data/test8_output.tsv --- a/test-data/test8_output.tsv Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,81 +0,0 @@ -Strand Read Position nMethylated nUnmethylated -OT 1 11 1 0 -OT 2 11 1 0 -OT 1 13 1 0 -OT 2 13 1 0 -OT 1 15 1 0 -OT 2 15 1 0 -OT 1 17 0 1 -OT 2 17 1 0 -OT 1 19 1 0 -OT 2 19 1 0 -OT 1 21 1 0 -OT 2 21 1 0 -OT 1 23 1 0 -OT 2 23 1 0 -OT 1 25 1 0 -OT 2 25 1 0 -OT 1 27 1 0 -OT 2 27 1 0 -OT 1 29 1 0 -OT 2 29 1 0 -OT 1 31 1 0 -OT 2 31 1 0 -OT 1 33 1 0 -OT 2 33 1 0 -OT 1 35 1 0 -OT 2 35 1 0 -OT 1 37 1 0 -OT 2 37 1 0 -OT 1 39 1 0 -OT 2 39 1 0 -OT 1 41 1 0 -OT 2 41 1 0 -OT 1 43 1 0 -OT 2 43 1 0 -OT 1 45 1 0 -OT 2 45 1 0 -OT 1 47 1 0 -OT 2 47 1 0 -OT 1 49 1 0 -OT 2 49 1 0 -OT 1 51 1 0 -OT 2 51 1 0 -OT 1 53 1 0 -OT 2 53 1 0 -OT 1 55 1 0 -OT 2 55 1 0 -OT 1 57 1 0 -OT 2 57 1 0 -OT 1 59 1 0 -OT 2 59 1 0 -OT 1 61 1 0 -OT 2 61 1 0 -OT 1 63 1 0 -OT 2 63 1 0 -OT 1 65 1 0 -OT 2 65 1 0 -OT 1 67 1 0 -OT 2 67 1 0 -OT 1 69 1 0 -OT 2 69 1 0 -OT 1 71 1 0 -OT 2 71 1 0 -OT 1 73 1 0 -OT 2 73 1 0 -OT 1 75 1 0 -OT 2 75 1 0 -OT 1 77 1 0 -OT 2 77 1 0 -OT 1 79 1 0 -OT 2 79 1 0 -OT 1 81 1 0 -OT 2 81 1 0 -OT 1 83 1 0 -OT 2 83 1 0 -OT 1 85 1 0 -OT 2 85 1 0 -OT 1 87 1 0 -OT 2 87 1 0 -OT 1 89 1 0 -OT 2 89 1 0 |
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| diff -r 183cb55b1729 -r d6787bab7b11 test-data/test_1.bedGraph --- a/test-data/test_1.bedGraph Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,49 +0,0 @@ -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 |
| b |
| diff -r 183cb55b1729 -r d6787bab7b11 test-data/test_2.bedGraph --- a/test-data/test_2.bedGraph Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -track type="bedGraph" description="output CHH methylation levels" -chrCG 98 99 100 1 0 |
| b |
| diff -r 183cb55b1729 -r d6787bab7b11 test-data/test_2_output.svg --- a/test-data/test_2_output.svg Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 183cb55b1729 -r d6787bab7b11 test-data/test_3.bedGraph --- a/test-data/test_3.bedGraph Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,49 +0,0 @@ -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 |
| b |
| diff -r 183cb55b1729 -r d6787bab7b11 test-data/test_4.bedGraph --- a/test-data/test_4.bedGraph Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,49 +0,0 @@ -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 |
| b |
| diff -r 183cb55b1729 -r d6787bab7b11 test-data/test_5.methylKit --- a/test-data/test_5.methylKit Fri Aug 24 17:15:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,49 +0,0 @@ -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 |
