pileometh: MethylDackel.xml annotate

annotate MethylDackel.xml @ 6:906db57d5d65 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d

author	bgruening
date	Tue, 13 Jun 2017 01:01:31 -0400
parents	f112bf3dd5ff
children	15df15127c18

rev	line source
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	1 <tool id="pileometh" name="MethylDackel" version="0.3.0">
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 <stdio>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	7 <!-- Anything other than zero is an error -->
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	8 <exit_code range="1:" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	9 <exit_code range=":-1" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	10 <!-- In case the return code has not been set propery check stderr too -->
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	11 <regex match="Error:" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	12 <regex match="Exception:" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	13 </stdio>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	14 <version_command><![CDATA[MethylDackel --version]]></version_command>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	15 <command><![CDATA[
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	16 #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	17 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	18 #else:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	19 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	20 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	21
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	22 MethylDackel
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	23 $main_task.task
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	24
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	25 -@ \${GALAXY_SLOTS:-4}
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	26 #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	27 -o output
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	28 $main_task.mergeContext
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	29 #if str($main_task.OT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	30 --OT $main_task.OT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	31 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	32 #if str($main_task.OB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	33 --OB $main_task.OB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	34 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	35 #if str($main_task.CTOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	36 --CTOT $main_task.CTOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	37 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	38 #if str($main_task.CTOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	39 --CTOB $main_task.CTOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	40 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	41 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	42
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	43 #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	44 #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	45 -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	46 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	47 $advanced_options.keepDupes
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	48 $advanced_options.keepSingleton
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	49 $advanced_options.keepDiscordant
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	50 -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	51 -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	52 -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	53 #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	54 --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	55 --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	56 -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	57 --ignoreFlags $advanced_options.ignoreFlags
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	58 --requireFlags $advanced_options.requireFlags
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	59 $advanced_options.fraction
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	60 $advanced_options.counts
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	61 $advanced_options.methylKit
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	62 $advanced_options.logit
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	63 #if str($advanced_options.nOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	64 --nOT $advanced_options.nOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	65 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	66 #if str($advanced_options.nOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	67 --nOB $advanced_options.nOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	68 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	69 #if str($advanced_options.nCTOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	70 --nCTOT $advanced_options.nCTOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	71 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	72 #if str($advanced_options.nCTOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	73 --nCTOB $advanced_options.nCTOB
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 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	76 $advanced_options.CHG
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	77 $advanced_options.CHH
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	78 #end if
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 reference.fasta
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	81
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	82 $input_sortedAlignBAM
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	83
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	84 #if $main_task.task == "mbias":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	85 out_mbias &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	86 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	87 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	88 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	89 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	90 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	91 ]]></command>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	92 <inputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	93 <conditional name="reference_source">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	94 <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	95 <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	96 <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	97 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	98 <when value="cached">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	99 <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	100 <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	101 <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	102 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	103 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	104 <when value="history">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	105 <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	106 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	107 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	108
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	109 <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	110 <conditional name="main_task">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	111 <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	112 <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	113 <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	114 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	115 <when value="extract">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	116 <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	117 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	118 <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	119 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	120 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	121 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	122 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	123 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	124 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	125 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	126 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	127 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	128 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	129 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	130 <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	131 <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	132 <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	133 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	134 <when value="mbias"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	135 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	136 <conditional name="advanced_options">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	137 <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	138 <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	139 <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	140 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	141 <when value="yes">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	142 <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation"/>
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"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	153 help="Minimum per-base dpeth for reporting output. If you use --mergeContext (above), then this applies to the merged CpG/CHG (default 1). (-d)" />
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
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	173 <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	174 label="Additional output file with CHG methylation metrics" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	175 <param name="CHH" type="boolean" checked="false" truevalue="--CHH" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	176 label="Additional output file with CHH methylation metrics" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	177
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	178 <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	179 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	180 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	181 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	182 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	183 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	184 <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	185 <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	186 <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	187 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	188 <when value=""/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	189 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	190 </inputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	191 <outputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	192 <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	193 label="${tool.name} on ${on_string}">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	194 <filter>main_task['task'] == "extract"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	195 <filter>not advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	196 <filter>not advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	197 <filter>not advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	198 <filter>not advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	199 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	200 <data name="outFileExtractCpGLogit" format="bedgraph" from_work_dir="output_CpG.logit.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	201 label="${tool.name} on ${on_string} (logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	202 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	203 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	204 <data name="outFileExtractCpGMethylKit" format="text" from_work_dir="output_CpG.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	205 label="${tool.name} on ${on_string} (MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	206 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	207 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	208 <data name="outFileExtractCpGCounts" format="bedgraph" from_work_dir="output_CpG.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	209 label="${tool.name} on ${on_string} (counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	210 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	211 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	212 <data name="outFileExtractCpGFraction" format="bedgraph" from_work_dir="output_CpG.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	213 label="${tool.name} on ${on_string} (fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	214 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	215 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	216 <data name="outFileExtractCHG" format="bedgraph" from_work_dir="output_CHG.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	217 label="${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	218 <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	219 <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	220 <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	221 <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	222 <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	223 <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	224 <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	225 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	226 <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	227 label="${tool.name} on ${on_string} (CHG logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	228 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	229 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	230 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	231 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	232 <data name="outFileExtractCHGMethylKit" format="text" from_work_dir="output_CHG.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	233 label="${tool.name} on ${on_string} (CHG MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	234 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	235 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	236 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	237 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	238 <data name="outFileExtractCHGCounts" format="bedgraph" from_work_dir="output_CHG.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	239 label="${tool.name} on ${on_string} (CHG counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	240 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	241 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	242 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	243 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	244 <data name="outFileExtractCHGFraction" format="bedgraph" from_work_dir="output_CHG.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	245 label="${tool.name} on ${on_string} (CHG fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	246 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	247 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	248 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	249 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	250 <data name="outFileExtractCHH" format="bedgraph" from_work_dir="output_CHH.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	251 label="${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	252 <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	253 <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	254 <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	255 <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	256 <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	257 <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	258 <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	259 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	260 <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	261 label="${tool.name} on ${on_string} (CHH logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	262 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	263 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	264 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	265 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	266 <data name="outFileExtractCHHMethylKit" format="text" from_work_dir="output_CHH.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	267 label="${tool.name} on ${on_string} (CHH MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	268 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	269 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	270 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	271 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	272 <data name="outFileExtractCHHCounts" format="bedgraph" from_work_dir="output_CHH.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	273 label="${tool.name} on ${on_string} (CHH counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	274 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	275 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	276 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	277 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	278 <data name="outFileExtractCHHFraction" format="bedgraph" from_work_dir="output_CHH.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	279 label="${tool.name} on ${on_string} (CHH fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	280 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	281 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	282 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	283 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	284 <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	285 label="${tool.name} on ${on_string} (methylation bias, original top strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	286 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	287 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	288 <data name="outFileMbiasCpGOB" format="svg" from_work_dir="out_mbias_OB.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	289 label="${tool.name} on ${on_string} (methylation bias, original bottom strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	290 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	291 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	292 <data name="outFileMbiasCpGCTOT" format="svg" from_work_dir="out_mbias_CTOT.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	293 label="${tool.name} on ${on_string} (methylation bias, complementary to the original top strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	294 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	295 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	296 <data name="outFileMbiasCpGCTOB" format="svg" from_work_dir="out_mbias_CTOB.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	297 label="${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	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 </outputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	301 <tests>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	302 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	312 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	321 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	334 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	344 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	354 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	364 </tests>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	365 <help><![CDATA[
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	366
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	367 .. 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	368 :align: left
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	369
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	370 What it does
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	371
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	372 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	373
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	374 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	375
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	376 Methylation context
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	377
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	378 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	379
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	380
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	381 Output information
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	382
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	383 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	384
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	385 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	386
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	387 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	388 2. The start coordinate
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	389 3. The end coordinate
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	390 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	391 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	392 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	393
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	394 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	395
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	396 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	397
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	398 #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	399 #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	400 #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	401
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	402 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	403
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	404 Per-CpG/CHG metrics
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	405
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	406 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	407
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	408 #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	409 #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	410 #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	411
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	412 is changed to this::
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 #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	415 #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	416
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	417 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	418
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	419 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	420
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	421 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	422
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	423 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	424 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	425
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	426 .. 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	427
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	428
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	429 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	430
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	431 Excluding low-coverage regions
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 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	434
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	435 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	436
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	437 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	438
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	439 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	440
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	441 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	442
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	443 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	444
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	445 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	446
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	447 methylKit-compatible output
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	448
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	449 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	450
6 906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	451 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	452
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	453 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	454
906db57d5d65 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 08bee869cbf7be7a70e2d7921ff42539bf5acd4d bgruening parents: 3 diff changeset	455 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	456
3 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 -----
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 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	461
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	462 .. _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	463 ]]></help>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	464 <citations>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	465 </citations>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	466 </tool>

Mercurial > repos > bgruening > pileometh

annotate MethylDackel.xml @ 6:906db57d5d65 draft