bismark: bismark_methylation_extractor.xml annotate

annotate bismark_methylation_extractor.xml @ 38:b2d0e92f81c2 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"

author	bgruening
date	Thu, 22 Apr 2021 17:05:07 +0000
parents	50c594522ed2
children

rev	line source
30 50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d bgruening parents: 29 diff changeset	1 <tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.22.1" profile="18.01">
25 a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	2 <description>Reports on methylation status of reads mapped by Bismark</description>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	3 <requirements>
30 50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d bgruening parents: 29 diff changeset	4 <requirement type="package" version="0.22.1">bismark</requirement>
25 a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	5 <requirement type="package" version="1.8">samtools</requirement>
30 50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d bgruening parents: 29 diff changeset	6 <requirement type="package" version="2.3.5">bowtie2</requirement>
25 a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	7 </requirements>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	8 <command><![CDATA[
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	9 python '$__tool_directory__/bismark_methylation_extractor.py'
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	10
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	11 --multicore "\${GALAXY_SLOTS:-4}"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	12
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	13 --infile '$input'
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	14
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	15 #if $singlePaired.sPaired == "single":
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	16 --single-end
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	17 #else:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	18 --paired-end
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	19 $singlePaired.no_overlap
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	20 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	21
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	22 #if str( $singlePaired['ignore_r1'] ) != "0":
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	23 --ignore $singlePaired['ignore_r1']
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	24 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	25 #if str( $singlePaired['ignore_3prime_r1'] ) != "0":
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	26 --ignore_3prime $singlePaired['ignore_3prime_r1']
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	27 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	28
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	29 #if $singlePaired.sPaired == "paired":
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	30 #if str( $singlePaired['ignore_r2'] ) != "0":
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	31 --ignore_r2 $singlePaired['ignore_r2']
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	32 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	33 #if str( $singlePaired['ignore_3prime_r2'] ) != "0":
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	34 --ignore_3prime_r2 $singlePaired['ignore_3prime_r2']
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	35 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	36 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	37
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	38 #if $splitting_report:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	39 --splitting_report '$output_splitting_report'
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	40 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	41
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	42 #if $mbias_report:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	43 --mbias_report '$output_mbias_report'
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	44 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	45
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	46 #if $cytosine_report['cytosine_report_selector']:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	47 --cytosine_report '$output_cytosine_report'
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	48 #if $cytosine_report.refGenomeSource.genomeSource == "built_in_fasta":
29 b52b7fdefd72 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8a26d7022e3535d995aec277e15d7d04800965e4 bgruening parents: 25 diff changeset	49 --genome_file '${cytosine_report.refGenomeSource.built_in_fasta.fields.path}'
25 a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	50 #else:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	51 --genome_file '$cytosine_report.refGenomeSource["own_file"]'
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	52 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	53 #if not $cytosine_report['cpg_context']:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	54 --cx_context
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	55 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	56 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	57
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	58 #if $output_settings['comprehensive']:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	59 --comprehensive
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	60 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	61
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	62 #if $output_settings['merge_non_cpg']:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	63 --merge-non-cpg
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	64 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	65
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	66 --compress '$compressed_output'
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	67
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	68 #if $output_settings['separate_logfile']:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	69 --log_report '$log_report'
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	70 #end if
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	71 ]]>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	72 </command>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	73 <inputs>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	74 <!-- Input Parameters -->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	75 <param name="input" type="data" format="qname_input_sorted.bam,bam,sam" label="SAM/BAM file from Bismark bisulfite mapper"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	76 <conditional name="singlePaired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	77 <param name="sPaired" type="select" label="Is this library mate-paired?">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	78 <option value="single">Single-end</option>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	79 <option value="paired">Paired-end</option>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	80 </param>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	81 <when value="single">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	82 <param name="ignore_r1" type="integer" value="0"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	83 label="Ignore the first N bp from the 5’ end of single-end read when processing the methylation call string."/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	84 <param name="ignore_3prime_r1" type="integer" value="0"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	85 label="Ignore the last N bp from the 3' end of single-end read when processing the methylation call string."/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	86 </when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	87 <when value="paired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	88 <param name="ignore_r1" type="integer" value="0"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	89 label="Ignore the first N bp from the 5’ end of Read 1 when processing the methylation call string."/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	90 <param name="ignore_3prime_r1" type="integer" value="0"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	91 label="Ignore the last N bp from the 3' end of Read 1 when processing the methylation call string."/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	92 <param name="ignore_r2" type="integer" value="0"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	93 label="Ignore the first N bp from the 5' end of Read 2 of paired-end sequencing results"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	94 <param name="ignore_3prime_r2" type="integer" value="0"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	95 label="Ignore the last N bp from the 3' end of Read 2 of paired-end sequencing results"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	96 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	97 label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	98 help=""/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	99 </when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	100 </conditional>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	101 <param name="splitting_report" type="boolean" truevalue="true" falsevalue="false" checked="True"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	102 label="Short methylation summary output (Splitting Report)"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	103 <param name="mbias_report" type="boolean" truevalue="true" falsevalue="false" checked="True"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	104 label="Methylation proportion report for each possible position in the read (Mbias Report)"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	105 <conditional name="cytosine_report">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	106 <param name="cytosine_report_selector" type="boolean" truevalue="true" falsevalue="false" checked="True"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	107 label="Genome-wide methylation report for all cytosines in the genome (Cytosine Report)"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	108 <when value="true">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	109 <conditional name="refGenomeSource">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	110 <param name="genomeSource" type="select"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	111 label="Will you select a reference genome from your history or use a built-in index?"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	112 help="Built-ins were indexed using default options">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	113 <option value="built_in_fasta">From built-in Reference Genome (fasta)</option>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	114 <option value="history">From Genome (fasta) in your Galaxy history</option>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	115 </param>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	116 <when value="built_in_fasta">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	117 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	118 <options from_data_table="all_fasta">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	119 <filter type="sort_by" column="name"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	120 <validator type="no_options"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	121 message="No genomes in fasta are available for the selected input dataset"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	122 </options>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	123 </param>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	124 </when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	125 <when value="history">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	126 <param name="own_file" type="data" format="fasta" label="Select the reference genome"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	127 </when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	128 </conditional>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	129 <param name="cpg_context" type="boolean" truevalue="true" falsevalue="false" checked="False"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	130 label="Reports Cpg Context only"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	131 </when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	132 <when value="false"></when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	133 </conditional>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	134 <section name="output_settings" title="Advanced output settings" expanded="False">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	135 <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="True"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	136 label="Merge all four possible strand-specific methylation info into context-dependent output files" help=""/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	137 <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	138 label="Merge all non-CpG contexts into one file"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	139 help="This will produce eight strand-specific output files, or two output files in comprehensive mode."/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	140 <param name="separate_logfile" type="boolean" truevalue="true" falsevalue="false" checked="False"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	141 label="Create a separate logfile, otherwise logs are added to the dataset info."/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	142 </section>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	143 </inputs>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	144 <outputs>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	145 <!--
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	146 OT – original top strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	147 CTOT – complementary to original top strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	148 OB – original bottom strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	149 CTOB – complementary to original bottom strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	150 -->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	151 <data format="tabular" name="output_splitting_report" label="${tool.name} on ${on_string}: Splitting Report">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	152 <filter>( splitting_report is True )</filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	153 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	154 <data format="txt" name="output_mbias_report" label="${tool.name} on ${on_string}: Mbias Report">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	155 <filter>( mbias_report is True )</filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	156 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	157 <data format="txt" name="output_cytosine_report"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	158 label="${tool.name} on ${on_string}: Genome-wide methylation report.">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	159 <filter>( cytosine_report['cytosine_report_selector'] )</filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	160 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	161 <data format="zip" name="compressed_output" label="${tool.name} on ${on_string}: Result archive."/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	162 <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	163 <filter>( output_settings['separate_logfile'] is True )</filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	164 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	165 </outputs>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	166 <tests>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	167 <test>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	168 <param name="input" value="mapped_reads.bam" ftype="qname_sorted.bam"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	169 <param name="sPaired" value="single"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	170 <param name="cytosine_report_selector" value="true"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	171 <param name="genomeSource" value="history"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	172 <param name="own_file" value="mm10.tiny.fa.gz" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	173
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	174 <param name="splitting_report" value="true"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	175 <param name="mbias_report" value="true"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	176
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	177 <output name="output_splitting_report" file="output_splitting_report.txt" ftype="tabular" lines_diff="2"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	178 <output name="output_mbias_report" file="output_mbias_report.txt" ftype="txt"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	179 <output name="output_cytosine_report">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	180 <assert_contents>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	181 <!-- is XML escape code for tab -->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	182 <has_line line="chrY_JH584303_random 4 + 0 0 CHH CAT" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	183 <has_line line="chrY_JH584301_random 259872 - 0 0 CHH CAT" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	184 </assert_contents>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	185 </output>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	186 </test>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	187 </tests>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	188
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	189 <help>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	190 <![CDATA[
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	191
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	192 What it does
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	193
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	194 \| The following is a brief description of all options to control the Bismark_methylation extractor. The script reads in a bisulfite read alignment results file produced by the Bismark bisulfite mapper and extracts the methylation information for individual cytosines. This information is found in the methylation call field which can contain the following characters:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	195 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	196
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	197
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	198 - X = for methylated C in CHG context (was protected)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	199 - x = for not methylated C CHG (was converted)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	200 - H = for methylated C in CHH context (was protected)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	201 - h = for not methylated C in CHH context (was converted)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	202 - Z = for methylated C in CpG context (was protected)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	203 - z = for not methylated C in CpG context (was converted)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	204 - . = for any bases not involving cytosines
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	205
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	206 \| The methylation extractor outputs result files for cytosines in CpG, CHG and CHH context (this distinction is actually already made in Bismark itself). As the methylation information for every C analysed can produce files which easily have tens or even hundreds of millions of lines, file sizes can become very large and more difficult to handle. The C methylation info additionally splits cytosine methylation calls up into one of the four possible strands a given bisulfite read aligned against:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	207 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	208
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	209 - OT = original top strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	210 - CTOT = complementary to original top strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	211
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	212 - OB = original bottom strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	213 - CTOB = complementary to original bottom strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	214
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	215 \| Thus, by default twelve individual output files are being generated per input file (unless --comprehensive is specified, see below). The output files can be imported into a genome viewer, such as SeqMonk, and re-combined into a single data group if desired (in fact unless the bisulfite reads were generated preserving directionality it doesn't make any sense to look at the data in a strand-specific manner). Strand-specific output files can optionally be skipped, in which case only three output files for CpG, CHG or CHH context will be generated. For both the strand-specific and comprehensive outputs there is also the option to merge both non-CpG contexts (CHG and CHH) into one single non-CpG context.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	216 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	217 \| It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	218
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	219 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	220
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	221 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	222
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	223 Outputs
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	224
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	225 - The output files are in the following format (tab delimited)::
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	226
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	227
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	228 Column Description
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	229 -------- --------------------------------------------------------
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	230 1 seq-ID
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	231 2 strand
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	232 3 chromosome
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	233 4 position
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	234 5 methylation call
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	235
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	236
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	237 - Methylated cytosines receive a '+' orientation,
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	238 - Unmethylated cytosines receive a '-' orientation.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	239
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	240 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	241
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	242 Note on Bismark settings
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	243
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	244 \| All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	245
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	246 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	247
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	248 Settings
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	249
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	250 * If Single-End Reads
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	251
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	252 * Ignore the first N bp from the 5’ end of single-end read when processing the methylation call string.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	253
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	254 \| This can remove e.g. a restriction enzyme site at the start of each read or any other source of bias (e.g. PBAT-Seq data).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	255 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	256 \| Input option --ignore <INT>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	257
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	258 * Ignore the last N bp from the 3' end of single-end read when processing the methylation call string.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	259
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	260 \| This can remove unwanted biases from the end of reads.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	261 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	262 \| Input option --ignore_3prime <INT>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	263
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	264 * If Paired-End Reads
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	265
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	266 * Ignore the first N bp from the 5’ end of Read 1 when processing the methylation call string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	267
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	268 \| This can remove e.g. a restriction enzyme site at the start of each read or any other source of bias (e.g. PBAT-Seq data).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	269 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	270 \| Input option --ignore <INT>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	271
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	272 * Ignore the last N bp from the 3’ end of Read 1 when processing the methylation call string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	273
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	274 \| This can remove unwanted biases from the end of reads.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	275 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	276 \| Input option --ignore_3prime <INT>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	277
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	278 * Ignore the first N bp from the 5' end of Read 2 of paired-end sequencing results
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	279
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	280 \| Since the first couple of bases in Read 2 of BS-Seq experiments show a severe bias towards non-methylation as a result of end-repairing sonicated fragments with unmethylated cytosines (see M-bias plot), it is recommended that the first couple of bp of Read 2 are removed before starting downstream analysis. Please see the section on M-bias plots in the Bismark User Guide for more details. The options --ignore <int> and --ignore_r2 <int> can be combined in any desired way.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	281 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	282 \| Input option --ignore_r2
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	283
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	284 * Ignore the last N bp from the 3' end of Read 2 of paired-end sequencing results
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	285
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	286 \| This can remove unwanted biases from the end of reads.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	287 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	288 \| Input option --ignore_3prime_r2
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	289
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	290 * This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	291
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	292 \| For paired-end reads it is theoretically possible that read_1 and read_2 overlap. This option avoids scoring overlapping methylation calls twice (only methylation calls of read 1 are used for in the process since read 1 has historically higher quality basecalls than read 2). Whilst this option removes a bias towards more methylation calls in the center of sequenced fragments it may de facto remove a sizable proportion of the data. This option is highly recommended for paired-end data.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	293 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	294 \| Input option --no_overlap
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	295
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	296 * Short methylation summary output (Splitting Report)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	297
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	298 \| Prints out a short methylation summary as well as the paramaters used to run this script.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	299 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	300 \| Output option --report
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	301
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	302 * Methylation proportion report for each possible position in the read (Mbias Report)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	303
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	304 \| This report shows the methylation proportion across each possible position in the read (described in further detail in:Hansen et al., Genome Biology, 2012, 13:R83). The data for the M-bias plot is also written into a text file and is in the following format:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	305 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	306 \| <read position> <count methylated> <count unmethylated> <% methylation> <total coverage>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	307 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	308 \| This allows generating nice graphs by alternative means, e.g. using R or Excel
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	309
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	310 * Genome-wide methylation report for all cytosines in the genome
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	311
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	312 \| the option --cytosine_report produces a genome-wide methylation report for all cytosines in the genome.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	313
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	314 * If CpG Context only
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	315
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	316 \| the output uses 1-based chromosome coordinates (zero-based cords are optional) and reports CpG context only (all cytosine context is optional). The output considers all Cs on both forward and reverse strands and reports their position, strand, trinucleotide content and methylation state (counts are 0 if not covered).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	317 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	318 \| Genome-wide cytosine methylation report specific option --bedgraph --cytosine_report --genome_folder <path>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	319
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	320 * If not CpG Context only
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	321
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	322 \| The output file contains information on every single cytosine in the genome irrespective of its context. This applies to both forward and reverse strands. Please be aware that this will generate output files with > 1.1 billion lines for a mammalian genome such as human or mouse. Default: OFF (i.e. Default = CpG context only).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	323 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	324 \| Genome-wide cytosine methylation report specific option --bedgraph --CX_context --cytosine_report --CX_context --genome_folder <path>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	325
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	326 * Merge all four possible strand-specific methylation info into context-dependent output files
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	327
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	328 \| Specifying this option will merge all four possible strand-specific methylation info into context-dependent output files. The default contexts are:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	329 \| - CpG context
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	330 \| - CHG context
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	331 \| - CHH context
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	332 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	333 \| Output option --comprehensive
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	334
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	335 * Merge all non-CpG contexts into one file
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	336
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	337 \| This will produce two output files (in --comprehensive mode) or eight strand-specific output files (default) for Cs in
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	338 \| - CpG context
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	339 \| - non-CpG context
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	340 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	341 \| Output option --merge_non_CpG
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	342
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	343 * Compress all result files and output one single file
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	344
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	345 \| The methylation extractor files (CpG_OT..., CpG_OB... etc) will be written out in a GZIP compressed form to save disk space. This option does not work on bedGraph and genome-wide cytosine reports as they are 'tiny' anyway.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	346 \|
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	347 \| Output option --gzip
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	348
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	349 ]]>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	350 </help>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	351
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	352 <citations>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	353 <citation type="doi">10.1093/bioinformatics/btr167</citation>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	354 </citations>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	355 </tool>

Mercurial > repos > bgruening > bismark

annotate bismark_methylation_extractor.xml @ 38:b2d0e92f81c2 draft default tip