pileometh: MethylDackel.xml annotate

annotate MethylDackel.xml @ 7:15df15127c18 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c

author	bgruening
date	Fri, 23 Mar 2018 17:52:57 -0400
parents	906db57d5d65
children	d6787bab7b11

rev	line source
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	1 <tool id="pileometh" name="MethylDackel" version="0.3.0.1">
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	2 <description>A tool for processing bisulfite sequencing alignments</description>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	3 <requirements>
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	4 <requirement type="package" version="0.3.0">methyldackel</requirement>
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	5 </requirements>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	6 <version_command><![CDATA[MethylDackel --version]]></version_command>
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	7 <command detect_errors="aggressive"><![CDATA[
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	8 #if $reference_source.reference_source_selector == "cached":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	9 ln -s $reference_source.ref_file.fields.path reference.fasta &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	10 #else:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	11 ln -s $reference_source.ref_file reference.fasta &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	12 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	13
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	14 MethylDackel
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	15 $main_task.task
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	16
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	17 -@ \${GALAXY_SLOTS:-4}
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	18 #if $main_task.task == "extract":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	19 -o output
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	20 $main_task.mergeContext
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	21 #if str($main_task.OT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	22 --OT $main_task.OT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	23 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	24 #if str($main_task.OB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	25 --OB $main_task.OB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	26 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	27 #if str($main_task.CTOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	28 --CTOT $main_task.CTOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	29 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	30 #if str($main_task.CTOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	31 --CTOB $main_task.CTOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	32 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	33 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	34
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	35 #if $advanced_options.options=="yes":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	36 #if $advanced_options.mbias_regionString:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	37 -r $advanced_options.mbias_regionString
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	38 #end if
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	39 #if $advanced_options.regionBed:
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	40 -l '$advanced_options.regionBed'
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	41 #end if
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	42 $advanced_options.keepDupes
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	43 $advanced_options.keepSingleton
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	44 $advanced_options.keepDiscordant
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	45 -q $advanced_options.min_mapq
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	46 -p $advanced_options.min_phred
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	47 -D $advanced_options.max_pbdepth
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	48 #if $main_task.task == "extract":
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	49 --minOppositeDepth $advanced_options.minOppositeDepth
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	50 --maxVariantFrac $advanced_options.maxVariantFrac
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	51 -d $advanced_options.min_pbdepth
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	52 --ignoreFlags $advanced_options.ignoreFlags
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	53 --requireFlags $advanced_options.requireFlags
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	54 $advanced_options.fraction
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	55 $advanced_options.counts
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	56 $advanced_options.methylKit
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	57 $advanced_options.logit
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	58 #if str($advanced_options.nOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	59 --nOT $advanced_options.nOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	60 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	61 #if str($advanced_options.nOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	62 --nOB $advanced_options.nOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	63 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	64 #if str($advanced_options.nCTOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	65 --nCTOT $advanced_options.nCTOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	66 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	67 #if str($advanced_options.nCTOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	68 --nCTOB $advanced_options.nCTOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	69 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	70 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	71 $advanced_options.CHG
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	72 $advanced_options.CHH
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	73 $advanced_options.noCpG
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	74 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	75
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	76 reference.fasta
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	77
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	78 $input_sortedAlignBAM
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	79
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	80 #if $main_task.task == "mbias":
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	81 out_mbias $main_task.tsv > out_mbias.tsv &&
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	82 touch out_mbias_OT.svg &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	83 touch out_mbias_OB.svg &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	84 touch out_mbias_CTOT.svg &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	85 touch out_mbias_CTOB.svg
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	86 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	87 ]]></command>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	88 <inputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	89 <conditional name="reference_source">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	90 <param name="reference_source_selector" type="select" label="Load reference genome from">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	91 <option value="cached">Local cache</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	92 <option value="history">History</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	93 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	94 <when value="cached">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	95 <param name="ref_file" type="select" label="Using reference genome" help="Reference sequence">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	96 <options from_data_table="all_fasta"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	97 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	98 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	99 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	100 <when value="history">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	101 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	102 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	103 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	104
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	105 <param name="input_sortedAlignBAM" multiple="False" type="data" format="bam" label="sorted_alignments.bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	106 <conditional name="main_task">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	107 <param name="task" type="select" label="What do you want to do?" >
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	108 <option value="extract">Extract methylation metrics from an alignment file in BAM/CRAM format</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	109 <option value="mbias">Determine the position-dependent methylation bias in a dataset, producing diagnostic SVG images</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	110 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	111 <when value="extract">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	112 <param name="mergeContext" type="boolean" checked="false" truevalue="--mergeContext" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	113 label="Merge per-Cytosine metrics from CpG and CHG contexts into per-CPG or per-CHG metrics" help="(--mergeContext)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	114 <param name="OT" type="text" value="" label="Original top strand bounds (comma-separated, no spaces)"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	115 help="Inclusion bounds for methylation calls from reads/pairs
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	116 origination from the original top strand. Suggested values can
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	117 be obtained from the MBias program. Each integer represents a
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	118 1-based position on a read. For example --OT A,B,C,D
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	119 translates to, 'Include calls at positions from A through B
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	120 on read #1 and C through D on read #2'. If a 0 is used a any
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	121 position then that is translated to mean start/end of the
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	122 alignment, as appropriate. For example, --OT 5,0,0,0 would
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	123 include all but the first 4 bases on read #1. Users are
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	124 strongly advised to consult a methylation bias plot, for
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	125 example by using the MBias program." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	126 <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	127 <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	128 <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	129 </when>
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	130 <when value="mbias">
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	131 <param name="tsv" type="boolean" truevalue="--txt" falsevalue=""
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	132 label="output tab separated mbias metrics"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	133 </when>
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	134 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	135 <conditional name="advanced_options">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	136 <param name="options" type="select" label="Advanced options">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	137 <option value="">Hide advanced options</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	138 <option value="yes">Display advanced options</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	139 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	140 <when value="yes">
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	141 <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation (e.g. chr1:1-100)"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	142 <param name="regionBed" type="data" optional="true" format='bed' label="Bed file of regions for inclusion"/>
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	143 <param name="keepDupes" type="boolean" checked="false" truevalue="--keepDupes" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	144 label="By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	145 <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	146 label="By default, if only one read in a pair aligns (a singleton) then it's ignored." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	147 <param name="keepDiscordant" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	148 label="By default, paired-end alignments with the properly-paired bit unset in the FLAG field are ignored. Note that the definition of concordant and discordant is based on your aligner settings." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	149 <param name="min_mapq" type="integer" value="10" label="Minimum MAPQ threshold to include an alignment (default 10)"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	150 <param name="min_phred" type="integer" value="5" label="Minimum Phred threshold to include a base (default 5). This must be >0."/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	151 <param name="max_pbdepth" type="integer" value="2000" label="Maximum per-base depth (default 2000)"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	152 <param name="min_pbdepth" type="integer" value="1" min="1" label="Minimum per-base depth"
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	153 help="Minimum per-base depth for reporting output. If you use --mergeContext (above), then this applies to the merged CpG/CHG (default 1). (-d)" />
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	154
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	155 <param name="ignoreFlags" type="integer" value="3840" label="Ignore certain alignments"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	156 help="By deault, any alignment marked as secondary (bit 0x100), failing QC (bit 0x200), a PCR/optical duplicate (0x400) or supplemental (0x800) is ignored. This equates to a value of 0xF00 or 3840 in decimal. If you would like to change that, you can specify a new value here." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	157 <param name="requireFlags" type="integer" value="0" label="Require alignment flags"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	158 help="Require each alignment to have all bits in this value present, or else the alignment is ignored. This is equivalent to the -f option in samtools. The default is 0, which includes all alignments." />
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	159 <param name="minOppositeDepth" type="integer" value="0" min="0" label="Minimum depth for variant avoidance"
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	160 help="The minimum depth on the strand opposite of a C required to flag the position as possibly being a SNP. The default is 0 (ignore possible SNPs). Setting this to a value above 0 will cause the position to be ignored if a given fraction of non-G bases are present on the opposite strand and the overall coverage there is at least what is specified here." />
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	161 <param name="maxVariantFrac" type="float" value="1.0" min="0.0" max="1.0" label="Maximum tolerated variant fraction"
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	162 help="If the depth on the strand opposite of a C is at least that specified by 'Minimum depth for variant avoidance', and the fraction of non-G bases exceeds this value, then methylation extraction is skipped for this position." />
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	163
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	164 <param name="fraction" type="boolean" checked="false" truevalue="--fraction" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	165 label="Extract fractional methylation (only) at each position. This is mutually exclusive with --counts, --logit, and --methylKit" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	166 <param name="counts" type="boolean" checked="false" truevalue="--counts" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	167 label="Extract base counts (only) at each position. This is mutually exclusive with --fraction, --logit, and --methylKit" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	168 <param name="logit" type="boolean" checked="false" truevalue="--logit" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	169 label="Extract logit(M/(M+U)) (only) at each position. This is mutually exclusive with --counts, --fraction, and --methylKit" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	170 <param name="methylKit" type="boolean" checked="false" truevalue="--methylKit" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	171 label="Output in the format required by methylKit. This is mutually exclusive with --counts, --fraction, and --logit" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	172
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	173 <param name="noCpG" type="boolean" checked="false" truevalue="--noCpG" falsevalue=""
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	174 label="Do not output CpG context methylation metrics" />
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	175 <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue=""
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	176 label="Output CHG context methylation metrics" />
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	177 <param name="CHH" type="boolean" checked="false" truevalue="--CHH" falsevalue=""
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	178 label="Output CHH context methylation metrics" />
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	179
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	180 <param name="nOT" type="text" value="" label="Original top strand absolute bounds (comma-separated, no spaces)"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	181 help="Like --OT, but always exclude INT bases from a given end
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	182 from inclusion,regardless of the length of an alignment. This
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	183 is useful in cases where reads may have already been trimmed
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	184 to different lengths, but still none-the-less contain a
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	185 certain length bias at one or more ends." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	186 <param name="nOB" type="text" value="" label="Original bottom strand absolute bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	187 <param name="nCTOT" type="text" value="" label="Complementary to the original bottom strand absolute bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	188 <param name="nCTOB" type="text" value="" label="Complementary to the original bottom strand absolute bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	189 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	190 <when value=""/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	191 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	192 </inputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	193 <outputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	194 <data name="outFileExtractCpG" format="bedgraph" from_work_dir="output_CpG.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	195 label="${tool.name} on ${on_string}">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	196 <filter>main_task['task'] == "extract"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	197 <filter>not advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	198 <filter>not advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	199 <filter>not advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	200 <filter>not advanced_options['fraction']</filter>
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	201 <filter>not advanced_options['noCpG']</filter>
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	202 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	203 <data name="outFileExtractCpGLogit" format="bedgraph" from_work_dir="output_CpG.logit.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	204 label="${tool.name} on ${on_string} (logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	205 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	206 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	207 <data name="outFileExtractCpGMethylKit" format="text" from_work_dir="output_CpG.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	208 label="${tool.name} on ${on_string} (MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	209 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	210 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	211 <data name="outFileExtractCpGCounts" format="bedgraph" from_work_dir="output_CpG.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	212 label="${tool.name} on ${on_string} (counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	213 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	214 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	215 <data name="outFileExtractCpGFraction" format="bedgraph" from_work_dir="output_CpG.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	216 label="${tool.name} on ${on_string} (fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	217 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	218 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	219 <data name="outFileExtractCHG" format="bedgraph" from_work_dir="output_CHG.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	220 label="${tool.name} on ${on_string} (CHG)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	221 <filter>main_task['task'] == 'extract'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	222 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	223 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	224 <filter>not advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	225 <filter>not advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	226 <filter>not advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	227 <filter>not advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	228 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	229 <data name="outFileExtractCHGLogit" format="bedgraph" from_work_dir="output_CHG.logit.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	230 label="${tool.name} on ${on_string} (CHG logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	231 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	232 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	233 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	234 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	235 <data name="outFileExtractCHGMethylKit" format="text" from_work_dir="output_CHG.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	236 label="${tool.name} on ${on_string} (CHG MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	237 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	238 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	239 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	240 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	241 <data name="outFileExtractCHGCounts" format="bedgraph" from_work_dir="output_CHG.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	242 label="${tool.name} on ${on_string} (CHG counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	243 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	244 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	245 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	246 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	247 <data name="outFileExtractCHGFraction" format="bedgraph" from_work_dir="output_CHG.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	248 label="${tool.name} on ${on_string} (CHG fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	249 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	250 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	251 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	252 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	253 <data name="outFileExtractCHH" format="bedgraph" from_work_dir="output_CHH.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	254 label="${tool.name} on ${on_string} (CHH)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	255 <filter>main_task['task'] == 'extract'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	256 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	257 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	258 <filter>not advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	259 <filter>not advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	260 <filter>not advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	261 <filter>not advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	262 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	263 <data name="outFileExtractCHHLogit" format="bedgraph" from_work_dir="output_CHH.logit.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	264 label="${tool.name} on ${on_string} (CHH logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	265 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	266 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	267 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	268 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	269 <data name="outFileExtractCHHMethylKit" format="text" from_work_dir="output_CHH.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	270 label="${tool.name} on ${on_string} (CHH MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	271 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	272 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	273 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	274 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	275 <data name="outFileExtractCHHCounts" format="bedgraph" from_work_dir="output_CHH.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	276 label="${tool.name} on ${on_string} (CHH counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	277 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	278 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	279 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	280 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	281 <data name="outFileExtractCHHFraction" format="bedgraph" from_work_dir="output_CHH.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	282 label="${tool.name} on ${on_string} (CHH fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	283 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	284 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	285 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	286 </data>
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	287 <data name="outFileMbiasTSV" format="tabular" from_work_dir="out_mbias.tsv"
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	288 label="${tool.name} on ${on_string} (methylation bias, tsv)">
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	289 <filter>main_task['task'] == 'mbias'</filter>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	290 <filter>main_task['tsv']</filter>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	291 </data>
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	292 <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	293 label="${tool.name} on ${on_string} (methylation bias, original top strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	294 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	295 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	296 <data name="outFileMbiasCpGOB" format="svg" from_work_dir="out_mbias_OB.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	297 label="${tool.name} on ${on_string} (methylation bias, original bottom strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	298 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	299 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	300 <data name="outFileMbiasCpGCTOT" format="svg" from_work_dir="out_mbias_CTOT.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	301 label="${tool.name} on ${on_string} (methylation bias, complementary to the original top strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	302 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	303 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	304 <data name="outFileMbiasCpGCTOB" format="svg" from_work_dir="out_mbias_CTOB.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	305 label="${tool.name} on ${on_string} (methylation bias, complementary to the original bottom strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	306 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	307 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	308 </outputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	309 <tests>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	310 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	311 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	312 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	313 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	314 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	315 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	316 <param name="mergeContext" value="false"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	317 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	318 <output name="outFileExtractCpG" file="test_1.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	319 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	320 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	321 <param name="task" value="mbias" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	322 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	323 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	324 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	325 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	326 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	327 <output name="outFileMbiasCpGOT" file="test_2_output.svg" ftype="svg" compare="diff"/>
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	328 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	329 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	330 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	331 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	332 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	333 <param name="CHH" value="True"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	334 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	335 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	336 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	337 <param name="mergeContext" value="false"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	338 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	339 <output name="outFileExtractCpG" file="test_1.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	340 <output name="outFileExtractCHH" file="test_2.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	341 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	342 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	343 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	344 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	345 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	346 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	347 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	348 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	349 <param name="fraction" value="true" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	350 <output name="outFileExtractCpGFraction" file="test_3.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	351 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	352 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	353 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	354 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	355 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	356 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	357 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	358 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	359 <param name="logit" value="true" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	360 <output name="outFileExtractCpGLogit" file="test_4.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	361 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	362 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	363 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	364 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	365 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	366 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	367 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	368 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	369 <param name="methylKit" value="true" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	370 <output name="outFileExtractCpGMethylKit" file="test_5.methylKit" ftype="text" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	371 </test>
7 15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	372 <test>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	373 <param name="task" value="mbias" />
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	374 <param name="min_mapq" value="2" />
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	375 <param name="options" value="yes"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	376 <param name="tsv" value="--txt"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	377 <param name="reference_source_selector" value="history" />
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	378 <param name="ref_file" value="cg100.fa" ftype="fasta" />
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	379 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	380 <output name="outFileMbiasTSV" file="test7_output.tsv" ftype="tabular" compare="diff"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	381 </test>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	382 <test>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	383 <param name="task" value="mbias" />
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	384 <param name="min_mapq" value="2" />
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	385 <param name="options" value="yes"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	386 <param name="regionBed" ftype="bed" value="cg100.bed"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	387 <param name="tsv" value="--txt"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	388 <param name="reference_source_selector" value="history" />
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	389 <param name="ref_file" value="cg100.fa" ftype="fasta" />
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	390 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	391 <output name="outFileMbiasTSV" file="test8_output.tsv" ftype="tabular" compare="diff"/>
15df15127c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c bgruening parents: 6 diff changeset	392 </test>
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	393 </tests>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	394 <help><![CDATA[
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	395
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	396 .. image:: $PATH_TO_IMAGES/MethylDackelLogo.png
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	397 :align: left
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	398
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	399 What it does
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	400
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	401 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.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	402
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	403 By default, MethylDackel will only calculate metrics for Cytosines in a CpG context, but metrics for those in CHG and CHH contexts are supported as well.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	404
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	405 Methylation context
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	406
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	407 MethylDackel groups all Cytosines into one of three sequence contexts: CpG, CHG, and CHH. Here, H is the IUPAC ambiguity code for any nucleotide other than G. If an N is encountered in the reference sequence, then the context will be assigned to CHG or CHH, as appropriate (e.g., CNG would be categorized as in a CHG context and CNC as in a CHH context). If a Cytosine is close enough to the end of a chromosome/contig such that its context can't be inferred, then it is categorized as CHH (e.g., a Cytosine as the last base of a chromosome is considered as being in a CHH context).
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	408
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	409
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	410 Output information
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	411
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	412 If no methylation can be found, the output will be empty.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	413
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	414 Otherwise a variant of bedGraph that's similar to the "coverage" file is produced. In short, each line consists of 6 tab separated columns:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	415
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	416 1. The chromosome/contig/scaffold name
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	417 2. The start coordinate
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	418 3. The end coordinate
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	419 4. The methylation percentage rounded to an integer
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	420 5. The number of alignments/pairs reporting methylated bases
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	421 6. The number of alignments/pairs reporting unmethylated bases
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	422
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	423 All coordinates are 0-based half open, which conforms to the bedGraph definition. When paired-end reads are aligned, it can often occur that their alignments overlap. In such cases, MethylDackel will not count both reads of the pair in its output, as doing so would lead to incorrect downstream statistical results.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	424
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	425 An example of the output is below::
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	426
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	427 #track type="bedGraph" description="SRR1182519.sorted CpG methylation levels"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	428 #1 25115 25116 100 3 0
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	429 #1 29336 29337 50 1 1
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	430
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	431 Note the header line, which starts with "track". The "description" field is used as a label in programs such as IGV. Each of the subsequent lines describe single Cytosines, the 25116th and 29337th base on chromosome 1, respectively. The first position has 3 alignments (or pairs of alignments) indicating methylation and 0 indicating unmethylation (100% methylation) and the second position has 1 alignment each supporting methylation and unmethylation (50% methylation).
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	432
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	433 Per-CpG/CHG metrics
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	434
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	435 In many circumstances, it's desireable for metrics from individual Cytosines in a CpG to be merged, producing per-CpG metrics rather than per-Cytosine metrics. This can be accomplished with the Merge per-Cytosine parameter. If this is used, then this output::
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	436
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	437 #track type="bedGraph" description="SRR1182519.sorted CpG methylation levels"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	438 #1 25114 25115 100 2 1
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	439 #1 25115 25116 100 3 0
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	440
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	441 is changed to this::
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	442
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	443 #track type="bedGraph" description="SRR1182519.sorted merged CpG methylation levels"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	444 #1 25114 25116 100 5 1
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	445
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	446 This also works for CHG-level metrics. If bedGraph files containing per-Cytosine metrics already exist, they can be converted to instead contain per-CpG/CHG metrics with MethylDackel mergeContext.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	447
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	448 Methylation bias plotting and correction
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	449
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	450 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.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	451
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	452 That command will create a methylation bias (mbias for short) plot for each of the strands for which there are valid alignments.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	453 The resulting mbias graphs are in SVG format and can be viewed in most modern web browsers:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	454
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	455 .. image:: $PATH_TO_IMAGES/example.svg
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	456
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	457
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	458 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!.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	459
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	460 Excluding low-coverage regions
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	461
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	462 If your downstream analysis requires an absolute minimum coverage (here, defined as the number of methylation calls kept after filtering for MAPQ, phred score, etc.), you can use the `--minDepth` option to achieve this. By default, `MethylDackel extract` will output all methylation metrics as long as the coverage is at least 1. If you use `--minDepth 10`, then only sites covered at least 10x will be output. This works in conjunction with the `--mergeContext` option, above. So if you request per-CpG context output (i.e., with `--mergeContext`) and `--minDepth 10` then only CpGs with a minimum coverage of 10 will be output.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	463
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	464 Logit, fraction, and counts only output
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	465
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	466 The standard output described above can be modified if you supply the `--fraction`, `--counts`, or `--logit` options to `MethylDackel extract`.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	467
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	468 The `--fraction` option essentially produces the first 4 columns of the standard output described above. The only other difference is that the range of the 4th column is now between 0 and 1, instead of 0 and 100. Instead of producing a file ending simply in `.bedGraph`, one ending in `.meth.bedGraph` will instead be produced.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	469
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	470 The `--counts` option produces the first three columns of the standard output followed by a column of total coverage counts. This last column is equivalent to the sum of the 5th and 6th columns of the standard output. The resulting file ends in `.counts.bedGraph` rather than simply `.bedGraph`.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	471
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	472 The `--logit` option produces the first three columns of the standard output followed by the logit transformed methylation fraction. The logit transformation is log(Methylation fraction/(1-Methylation fraction)). Note that log uses base e. Logit transformed methylation values range between +/- infinity, rather than [0,1]. The resulting file ends in `.logit.bedGraph` rather than simply `.bedGraph`.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	473
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	474 Note that these options may be combined with `--mergeContext`. However, `MethylDackel mergeContext` can not be used after the fact to combine these.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	475
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	476 methylKit-compatible output
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	477
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	478 methylKit has its own format, which can be produced with the `--methylKit` option. Merging Cs into CpGs or CHGs is forbidden in this format. Likewise, this option is mutually exclusive with `--logit` et al.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	479
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	480 Excluding likely variant sites
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	481
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	482 If your samples are not genetically homogenous, it can sometimes be advantageous to exclude likely variant sites from methylation extraction. As an example, since unmethylated Cs are read as Ts, extracting methylation from a position with a C->T mutation will cause incorrect results. In such a case, the opposite strand will have an A rather than a G (in the non-variant case, there would be a G regardless of methylation status). MethylDackel tracks the number of non-Gs on the strand opposite of Cs in the reference sequence. If the fraction of these exceeds the `--maxVariantFrac` option, then that position will be excluded from output. To exclude cases where the `--maxVariantFrac` value is exceeded only due to low coverage, the opposite strand must have a depth of coverage of at least `--minOppositeDepth`. Note that the default value for `--minOppositeDepth` is 0, indicating that the variant site exclusion process is skipped.
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	483
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	484 Note that if one additionally specifies `--mergeContext`, that a given CpG or CHG will be excluded from output if either of its individual Cs would be excluded given the specified `--minOppositeDepth` and `--maxVariantFrac`.
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	485
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	486
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	487 -----
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	488
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	489 MethylDackel is a Free and Open Source Software, see more details on the MethylDackel_ Website.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	490
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	491 .. _MethylDackel: https://github.com/dpryan79/MethylDackel
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	492 ]]></help>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	493 <citations>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	494 </citations>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	495 </tool>

Mercurial > repos > bgruening > pileometh

annotate MethylDackel.xml @ 7:15df15127c18 draft