pileometh: MethylDackel.xml annotate

annotate MethylDackel.xml @ 3:f112bf3dd5ff draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648

author	bgruening
date	Mon, 13 Feb 2017 22:44:01 -0500
parents
children	906db57d5d65

rev	line source
3 f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	1 <tool id="pileometh" name="MethylDackel" version="0.2.1">
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>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	4 <requirement type="package" version="0.2.1">methyldackel</requirement>
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
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	25 #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	26 -o output
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	27 $main_task.mergeContext
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	28 #if str($main_task.OT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	29 --OT $main_task.OT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	30 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	31 #if str($main_task.OB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	32 --OB $main_task.OB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	33 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	34 #if str($main_task.CTOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	35 --CTOT $main_task.CTOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	36 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	37 #if str($main_task.CTOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	38 --CTOB $main_task.CTOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	39 #end if
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
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	42 #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	43 #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	44 -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	45 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	46 $advanced_options.keepDupes
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	47 $advanced_options.keepSingleton
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	48 $advanced_options.keepDiscordant
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	49 -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	50 -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	51 -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	52 #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	53 -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	54 --ignoreFlags $advanced_options.ignoreFlags
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	55 --requireFlags $advanced_options.requireFlags
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	56 $advanced_options.fraction
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	57 $advanced_options.counts
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	58 $advanced_options.methylKit
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	59 $advanced_options.logit
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	60 #if str($advanced_options.nOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	61 --nOT $advanced_options.nOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	62 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	63 #if str($advanced_options.nOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	64 --nOB $advanced_options.nOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	65 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	66 #if str($advanced_options.nCTOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	67 --nCTOT $advanced_options.nCTOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	68 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	69 #if str($advanced_options.nCTOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	70 --nCTOB $advanced_options.nCTOB
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 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	73 $advanced_options.CHG
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	74 $advanced_options.CHH
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
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	77 reference.fasta
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	78
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	79 $input_sortedAlignBAM
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	80
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	81 #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	82 out_mbias &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	83 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	84 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	85 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	86 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	87 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	88 ]]></command>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	89 <inputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	90 <conditional name="reference_source">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	91 <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	92 <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	93 <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	94 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	95 <when value="cached">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	96 <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	97 <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	98 <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	99 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	100 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	101 <when value="history">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	102 <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	103 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	104 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	105
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	106 <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	107 <conditional name="main_task">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	108 <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	109 <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	110 <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	111 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	112 <when value="extract">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	113 <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	114 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	115 <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	116 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	117 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	118 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	119 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	120 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	121 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	122 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	123 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	124 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	125 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	126 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	127 <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	128 <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	129 <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	130 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	131 <when value="mbias"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	132 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	133 <conditional name="advanced_options">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	134 <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	135 <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	136 <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	137 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	138 <when value="yes">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	139 <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	140 <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	141 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	142 <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	143 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	144 <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	145 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	146 <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	147 <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	148 <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	149 <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	150 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	151
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	152 <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	153 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	154 <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	155 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." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	156
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	157 <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	158 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	159 <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	160 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	161 <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	162 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	163 <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	164 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	165
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	166 <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	167 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	168 <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	169 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	170
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	171 <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	172 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	173 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	174 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	175 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	176 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	177 <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	178 <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	179 <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	180 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	181 <when value=""/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	182 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	183 </inputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	184 <outputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	185 <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	186 label="${tool.name} on ${on_string}">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	187 <filter>main_task['task'] == "extract"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	188 <filter>not advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	189 <filter>not advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	190 <filter>not advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	191 <filter>not advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	192 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	193 <data name="outFileExtractCpGLogit" format="bedgraph" from_work_dir="output_CpG.logit.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	194 label="${tool.name} on ${on_string} (logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	195 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	196 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	197 <data name="outFileExtractCpGMethylKit" format="text" from_work_dir="output_CpG.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	198 label="${tool.name} on ${on_string} (MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	199 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	200 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	201 <data name="outFileExtractCpGCounts" format="bedgraph" from_work_dir="output_CpG.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	202 label="${tool.name} on ${on_string} (counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	203 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	204 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	205 <data name="outFileExtractCpGFraction" format="bedgraph" from_work_dir="output_CpG.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	206 label="${tool.name} on ${on_string} (fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	207 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	208 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	209 <data name="outFileExtractCHG" format="bedgraph" from_work_dir="output_CHG.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	210 label="${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	211 <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	212 <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	213 <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	214 <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	215 <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	216 <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	217 <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	218 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	219 <data name="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	220 label="${tool.name} on ${on_string} (CHG logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	221 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	222 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	223 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	224 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	225 <data name="outFileExtractCHGMethylKit" format="text" from_work_dir="output_CHG.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	226 label="${tool.name} on ${on_string} (CHG MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	227 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	228 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	229 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	230 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	231 <data name="outFileExtractCHGCounts" format="bedgraph" from_work_dir="output_CHG.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	232 label="${tool.name} on ${on_string} (CHG counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	233 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	234 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	235 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	236 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	237 <data name="outFileExtractCHGFraction" format="bedgraph" from_work_dir="output_CHG.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	238 label="${tool.name} on ${on_string} (CHG fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	239 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	240 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	241 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	242 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	243 <data name="outFileExtractCHH" format="bedgraph" from_work_dir="output_CHH.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	244 label="${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	245 <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	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	253 <data name="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	254 label="${tool.name} on ${on_string} (CHH logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	255 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	256 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	257 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	258 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	259 <data name="outFileExtractCHHMethylKit" format="text" from_work_dir="output_CHH.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	260 label="${tool.name} on ${on_string} (CHH MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	261 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	262 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	263 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	264 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	265 <data name="outFileExtractCHHCounts" format="bedgraph" from_work_dir="output_CHH.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	266 label="${tool.name} on ${on_string} (CHH counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	267 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	268 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	269 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	270 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	271 <data name="outFileExtractCHHFraction" format="bedgraph" from_work_dir="output_CHH.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	272 label="${tool.name} on ${on_string} (CHH fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	273 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	274 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	275 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	276 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	277 <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	278 label="${tool.name} on ${on_string} (methylation bias, original top strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	279 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	280 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	281 <data name="outFileMbiasCpGOB" format="svg" from_work_dir="out_mbias_OB.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	282 label="${tool.name} on ${on_string} (methylation bias, original bottom strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	283 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	284 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	285 <data name="outFileMbiasCpGCTOT" format="svg" from_work_dir="out_mbias_CTOT.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	286 label="${tool.name} on ${on_string} (methylation bias, complementary to the original top strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	287 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	288 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	289 <data name="outFileMbiasCpGCTOB" format="svg" from_work_dir="out_mbias_CTOB.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	290 label="${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	291 <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	292 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	293 </outputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	294 <tests>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	295 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	305 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <output name="outFileMbiasCpG" file="test_2_output.svg" ftype="svg" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	313 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	314 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	315 <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	316 <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	317 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	318 <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	319 <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	320 <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	321 <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	322 <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	323 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	324 <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	325 <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	326 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	327 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	337 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	347 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	357 </tests>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	358 <help><![CDATA[
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	359
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	360 .. 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	361 :align: left
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	362
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	363 What it does
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	364
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	365 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	366
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	367 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	368
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	369 Methylation context
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	370
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	371 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	372
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 Output information
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 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	377
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	378 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	379
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	380 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	381 2. The start coordinate
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	382 3. The end coordinate
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	383 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	384 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	385 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	386
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	387 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	388
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	389 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	390
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	391 #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	392 #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	393 #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	394
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	395 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	396
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	397 Per-CpG/CHG metrics
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	398
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	399 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	400
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	401 #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	402 #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	403 #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	404
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	405 is changed to this::
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	406
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	407 #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	408 #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	409
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	410 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	411
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	412 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	413
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	414 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	415
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	416 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	417 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	418
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	419 .. 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	420
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	421
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	422 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	423
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	424 Excluding low-coverage regions
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 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	427
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	428 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	429
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	430 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	431
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	432 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	433
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	434 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	435
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	436 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	437
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	438 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	439
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	440 methylKit-compatible output
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	441
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	442 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	443
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 -----
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 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	448
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	449 .. _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	450 ]]></help>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	451 <citations>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	452 </citations>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648 bgruening parents: diff changeset	453 </tool>

Mercurial > repos > bgruening > pileometh

annotate MethylDackel.xml @ 3:f112bf3dd5ff draft