deeptools_multi_bam_summary: deepTools

annotate deepTools_macros.xml @ 19:c7ac0b77d00a draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e071ca1cc84da473ecc209c9d5e633d90cbc6a78

author	bgruening
date	Mon, 15 May 2017 03:55:48 -0400
parents	50da5a8ab41d
children	955d91e713d5

rev	line source
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	1 <macros>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	2
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
19 c7ac0b77d00a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e071ca1cc84da473ecc209c9d5e633d90cbc6a78 bgruening parents: 18 diff changeset	4 <token name="@WRAPPER_VERSION@">2.5.1.1</token>
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	5 <xml name="requirements">
d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	6 <requirements>
19 c7ac0b77d00a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e071ca1cc84da473ecc209c9d5e633d90cbc6a78 bgruening parents: 18 diff changeset	7 <requirement type="package" version="2.5.1">deeptools</requirement>
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	8 <yield />
d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	9 </requirements>
d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	10 <expand macro="stdio" />
d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	11 <version_command>@BINARY@ --version</version_command>
d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	12 </xml>
d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	13
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	14 <xml name="advancedOpt_scaffold">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	15 <conditional name="advancedOpt">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	16 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	17 <option value="no" selected="true">no</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	18 <option value="yes">yes</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	19 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	20 <when value="no" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	21 <when value="yes">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	22 <yield/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	23 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	24 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	25 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	26
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	27 <token name="@PLOTWIDTHHEIGHT@">
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	28 --plotWidth '$advancedOpt.plotWidth'
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	29 --plotHeight '$advancedOpt.plotHeight'
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	30 </token>
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	31
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	32 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	33 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	34 label="Plot height"
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	36
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	37 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	38 label="Plot width"
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	39 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	40 </xml>
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	41
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	42 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	43 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	44 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	45 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	46 --extendReads
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	47 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	48 $advancedOpt.ignoreDuplicates
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	49 $advancedOpt.centerReads
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	50 #if $advancedOpt.minMappingQuality:
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	51 --minMappingQuality '$advancedOpt.minMappingQuality'
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	52 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	53 #if $advancedOpt.samFlagInclude:
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	54 --samFlagInclude $advancedOpt.samFlagInclude
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	55 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	56 #if $advancedOpt.samFlagExclude:
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	57 --samFlagExclude $advancedOpt.samFlagExclude
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	58 #end if
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	59 #if $advancedOpt.minFragmentLength:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	60 --minFragmentLength $advancedOpt.minFragmentLength
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	61 #end if
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	62 #if $advancedOpt.maxFragmentLength:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	63 --maxFragmentLength $advancedOpt.maxFragmentLength
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	64 #end if
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	65 </token>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	66
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	67 <token name="@ADVANCED_OPTS_GTF@">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	68 $advancedOpt.metagene
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	69 #if $advancedOpt.transcriptID:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	70 --transcriptID $advancedOpt.transcriptID
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	71 #end if
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	72 #if $advancedOpt.exonID:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	73 --exonID $advancedOpt.exonID
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	74 #end if
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	75 #if $advancedOpt.transcript_id_designator:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	76 --transcript_id_designator $advancedOpt.transcript_id_designator
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	77 #end if
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	78 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	79
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	80 <xml name="heatmap_options">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	81 <expand macro="zMin_zMax" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	82 <expand macro="colorMap" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	83 <expand macro="plotTitle" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	84 <expand macro="plotNumbers" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	85 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	86
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	87 <token name="@HEATMAP_OPTIONS@">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	88 #if str($plotting_type.zMin) != "":
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	89 --zMin $plotting_type.zMin
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	90 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	91 #if str($plotting_type.zMax) != "":
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	92 --zMax $plotting_type.zMax
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	93 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	94 --colorMap '$plotting_type.colorMap'
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	95 $plotting_type.plotNumbers
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	96 --plotTitle '$plotting_type.plotTitle'
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	97 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	98
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	99
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	100 <xml name="includeZeros">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	101 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	102 label="Include zeros"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	103 help="If set, then regions with zero counts for all BAM files are included. The default behavior is to ignore such regions." />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	104 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	105
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	106 <xml name="zMin_zMax">
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	107 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	108 help="If not specified the value is set automatically."/>
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	109 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	110 help="If not specified the value is set automatically."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	111 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	112
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	113 <xml name="region_limit_operation">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	114 <param argument="--region" type="text" value=""
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	115 label="Region of the genome to limit the operation to"
8 3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	116 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".">
3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	117 <sanitizer>
3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	118 <valid initial="string.letters,string.digits">
3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	119 <add value="\|"/>
12 bb00146fa60a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 11 diff changeset	120 <add value=":"/>
8 3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	121 </valid>
3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	122 </sanitizer>
3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	123 </param>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	124 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	125
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	126 <xml name="smoothLength">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	127 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	128 label="Smooth values using the following length (in bases)"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	129 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	130 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	131
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	132
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	133 <xml name="kmeans_clustering">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	134 <conditional name="used_multiple_regions">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	135 <param name="used_multiple_regions_options" type="select"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	136 label="Did you compute the matrix with more than one groups of regions?"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	137 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	138 <option value="yes">Yes, I used multiple groups of regions</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	139 <option value="no">No, I used only one group</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	140 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	141 <when value="no">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	142 <conditional name="clustering">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	143 <param name="clustering_options" type="select" label="Clustering algorithm">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	144 <option value="none">No clustering</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	145 <option value="kmeans">Kmeans clustering</option>
2 46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	146 <option value="hclust">Hierarchical clustering</option>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	147 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	148 <when value="kmeans">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	149 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	150 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	151 This only works for data that is not grouped, otherwise only the first group will be clustered.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	152 If more specific clustering methods are required it is advisable to save the underlying matrix and
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	153 run the clustering using other software."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	154 </when>
2 46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	155 <when value="hclust">
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	156 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	157 help="WARNING: This option causes the tool to run for a very long time! When this option is
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	158 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	159 This only works for data that is not grouped, otherwise only the first group will be clustered.
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	160 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	161 If more specific clustering methods are required it is advisable to save the underlying matrix and
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	162 run the clustering using other software."/>
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	163 </when>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	164 <when value="none" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	165 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	166 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	167 <when value="yes" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	168 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	169 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	170
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	171 <token name="@KMEANS_CLUSTERING@">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	172 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	173 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	174 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	175 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	176 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	177 #end if
2 46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	178 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	179 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	180 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	181 #end if
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	182 #end if
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	183 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	184 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	185
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	186 <xml name="samFlags">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	187 <param argument="--samFlagInclude" type="integer" optional="True" value=""
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	188 label="Include reads based on the SAM flag"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	189 help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	190 <param argument="--samFlagExclude" type="integer" optional="True" value=""
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	191 label="Exclude reads based on the SAM flag"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	192 help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	193 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	194
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	195 <xml name="fragLength">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	196 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	197 label="Minimum fragment length for inclusion."
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	198 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	199 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	200 label="Maximum fragment length for inclusion."
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	201 help="A value of 0 (the default) is equivalent to no maximum." />
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	202 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	203
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	204 <xml name="read_processing_options">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	205 <expand macro="extendReads" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	206 <expand macro="ignoreDuplicates" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	207 <expand macro="centerReads" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	208 <expand macro="minMappingQuality" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	209 <expand macro="samFlags" />
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	210 <expand macro="fragLength" />
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	211 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	212
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	213 <xml name="gtf_options">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	214 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	215 label="Use a metagene model"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	216 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	217 <param argument="--transcriptID" optional="True" value="transcript" type="text"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	218 label="trascript designator"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	219 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	220 <param argument="--exonID" optional="True" value="exon" type="text"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	221 label="exon designator"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	222 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	223 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	224 label="transcriptID key designator"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	225 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	226 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	227 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	228 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	229 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	230
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	231
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	232 <xml name="plotNumbers">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	233 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	234 label="Plot the correlation value"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	235 help="If set, then the correlation number is plotted on top of the heatmap."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	236 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	237
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	238 <xml name="extendReads">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	239 <conditional name="doExtendCustom">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	240 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	241 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	242 By default each read mate is extended.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	243 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	244 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	245 Reads are only extended if --extendReads is set to a value greater than the read length. NOTE: For spliced-read data, this option is not
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	246 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	247 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	248 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	249 <option value="custom">A custom length, which will be applied to ALL reads.</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	250 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	251 <when value="no" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	252 <when value="yes" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	253 <when value="custom">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	254 <param name="extendReadsValue" type="integer" value="300" min="1"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	255 label="Extend reads to the given average fragment size"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	256 help="Extend all reads to this length" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	257 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	258 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	259 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	260
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	261 <xml name="corMethod">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	262 <param argument="--corMethod" type="select" label="Correlation method">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	263 <option value="spearman" selected="True">Spearman</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	264 <option value="pearson">Pearson</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	265 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	266 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	267
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	268 <xml name="distanceBetweenBins">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	269 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	270 label="Distance between bins"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	271 help="By default, multiBamSummary considers consecutive bins of
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	272 the specified 'Bin size'. However, to reduce the
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	273 computation time, a larger distance between bins can
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	274 be given. Larger distances result in fewer bins being
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	275 considered."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	276 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	277
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	278 <xml name="centerReads">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	279 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	280 label="Center regions with respect to the fragment length"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	281 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	282 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	283
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	284 <xml name="ignoreDuplicates">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	285 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	286 label="Ignore duplicates"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	287 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	288 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	289
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	290 <xml name="sortUsing">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	291 <param argument="--sortUsing" type="select" label="Method used for sorting"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	292 help="For each row the method is computed.">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	293 <option value="mean" selected="true">mean</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	294 <option value="median">median</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	295 <option value="min">min</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	296 <option value="max">max</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	297 <option value="sum">sum</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	298 <option value="region_length">region length</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	299 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	300 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	301
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	302 <xml name="sortRegionsComputeMatrix">
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	303 <param argument="--sortRegions" type="select" label="Sort regions"
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	304 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	305 <option value="no">no ordering</option>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	306 <option value="keep" selected="true">maintain the same ordering as the input files</option>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	307 <option value="descend">descending order</option>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	308 <option value="ascend">ascending order</option>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	309 </param>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	310 </xml>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	311
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	312 <xml name="sortRegions">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	313 <param argument="--sortRegions" type="select" label="Sort regions"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	314 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	315 <option value="no">no ordering</option>
15 ef0cc90a66b8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 14 diff changeset	316 <option value="descend" selected="true">descending order</option>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	317 <option value="ascend">ascending order</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	318 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	319 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	320
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	321 <xml name="minMappingQuality">
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	322 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	323 label="Minimum mapping quality"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	324 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	325 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	326
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	327 <xml name="skipZeros">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	328 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	329 label ="Skip zeros"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	330 help ="If set, then zero counts that happen for all BAM files given are ignored. This may result in fewer considered regions." />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	331 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	332
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	333 <xml name="fragmentLength">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	334 <param argument="--fragmentLength" type="integer" value="300" min="1"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	335 label="Fragment length used for the sequencing"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	336 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	337 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	338
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	339 <xml name="scaleFactor">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	340 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	341 help="The computed scaling factor will be multiplied by this (default 1)." />
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	342 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	343
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	344 <xml name="scaleFactors">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	345 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	346 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	347 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	348
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	349 <xml name="stdio">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	350 <stdio>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	351 <exit_code range="1:" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	352 <exit_code range=":-1" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	353 <regex match="Error:" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	354 <regex match="Exception:" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	355 <regex match="EXception:" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	356 <regex match="Traceback" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	357 </stdio>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	358 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	359
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	360 <xml name="pseudocount">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	361 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	362 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	363
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	364 <token name="@REFERENCES@">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	365
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	366 .. class:: infomark
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	367
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	368 For more information on the tools, please visit our `help site`_.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	369
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	370 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	371
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	372 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	373
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	374 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	375 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	376 .. _help site: https://deeptools.readthedocs.org/
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	377
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	378 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	379 <xml name="citations">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	380 <citations>
8 3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	381 <citation type="doi">10.1093/nar/gkw257</citation>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	382 <yield />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	383 </citations>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	384 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	385
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	386 <xml name="multiple_input_bams" tokens="MIN">
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	387 <conditional name="multibam_conditional">
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	388 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	389 <option value="No" selected="true">No</option>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	390 <option value="Yes">Yes</option>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	391 </param>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	392 <when value="No">
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	393 <param argument="--bamfiles" type="data" format="bam" min="@MIN@"
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	394 label="Bam file" multiple="true"
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	395 help=""/>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	396 </when>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	397 <when value="Yes">
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	398 <repeat name="multibam_repeats" min="@MIN@" title="BAM Files">
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	399 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	400 </repeat>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	401 </when>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	402 </conditional>
3 41c2e05aa70c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 2 diff changeset	403 </xml>
41c2e05aa70c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 2 diff changeset	404
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	405 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	406 <conditional name="multibigwig_conditional">
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	407 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	408 is vital to you, select Yes below.">
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	409 <option value="No" selected="true">No</option>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	410 <option value="Yes">Yes</option>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	411 </param>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	412 <when value="No">
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	413 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	414 label="@LABEL@"
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	415 help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	416 </when>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	417 <when value="Yes">
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	418 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	419 <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	420 </repeat>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	421 </when>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	422 </conditional>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	423 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	424
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	425 <xml name="plotTitle">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	426 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	427 label="Title of the plot"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	428 help="Title of the plot, to be printed on top of the generated image." />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	429 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	430
2 46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	431
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	432 <token name="@multiple_input_bams@">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	433 <![CDATA[
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	434 #set files=[]
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	435 #set labels=[]
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	436 #import re
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	437 #if $multibam_conditional.orderMatters == "No":
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	438 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	439 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	440 ln -s "${bamfile}" "./${counter}.bam" &&
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	441 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	442 #silent $files.append('%s.bam' % $counter)
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	443 #silent $labels.append("'%s'" % identifier)
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	444 #end for
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	445 #else:
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	446 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	447 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
15 ef0cc90a66b8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 14 diff changeset	448 ln -s "${f.bamfiles}" "./${counter}.bam" &&
ef0cc90a66b8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 14 diff changeset	449 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	450 #silent $files.append('%s.bam' % $counter)
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	451 #silent $labels.append("'%s'" % $identifier)
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	452 #end for
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	453 #end if
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	454 ]]>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	455 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	456
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	457 <token name="@multiple_input_bigwigs@">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	458 <![CDATA[
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	459 #set files=[]
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	460 #set labels=[]
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	461 #import re
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	462 #if $multibigwig_conditional.orderMatters == "No":
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	463 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	464 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	465 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	466 #silent $files.append('%s_%s.bw' % ($identifier, $counter))
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	467 #silent $labels.append("'%s'" % $identifier)
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	468 #end for
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	469 #else:
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	470 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	471 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	472 ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	473 #silent $files.append('%s_%s.bw' % ($identifier, $counter))
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	474 #silent $labels.append("'%s'" % $identifier)
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	475 #end for
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	476 #end if
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	477 ]]>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	478 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	479
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	480 <xml name="blacklist">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	481 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	482 label="Blacklisted regions in BED/GTF format"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	483 help="One or more files containing regions to exclude from the analysis" />
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	484 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	485
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	486 <token name="@blacklist@">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	487 <![CDATA[
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	488 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	489 #set blfiles=[]
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	490 #for $f in $advancedOpt.blackListFileName:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	491 #silent $blfiles.append("'%s'" % $f)
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	492 #end for
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	493 #if $blfiles != ["'None'"]:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	494 --blackListFileName #echo ' '.join($blfiles)#
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	495 #end if
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	496 #end if
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	497 ]]>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	498 </token>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	499
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	500 <xml name="multiple_bed">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	501 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	502 label="Regions in BED/GTF format"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	503 help="One or more files containing regions to include in the analysis" />
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	504 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	505
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	506 <token name="@multiple_bed@">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	507 <![CDATA[
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	508 #set files=[]
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	509 #set labels=[]
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	510 #for $f in $BED:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	511 #silent $files.append("'%s'" % $f)
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	512 #silent $labels.append("'%s'" % $f.display_name)
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	513 #end for
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	514 #if len($files) > 0:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	515 --BED #echo ' '.join($files)#
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	516 --regionLabels #echo ' '.join($labels)#
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	517 #end if
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	518 ]]>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	519 </token>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	520
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	521 <xml name="reference_genome_source">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	522 <conditional name="source">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	523 <param name="ref_source" type="select" label="Reference genome">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	524 <option value="cached">locally cached</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	525 <option value="history">in your history</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	526 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	527 <when value="cached">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	528 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	529 <options from_data_table="lastz_seqs">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	530 <filter type="sort_by" column="1" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	531 <validator type="no_options" message="No indexes are available." />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	532 </options>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	533 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	534 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	535 <when value="history">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	536 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	537 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	538 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	539 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	540
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	541 <token name="@reference_genome_source@">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	542 #if $source.ref_source=="history":
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	543 --genome $source.input1
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	544 #else:
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	545 --genome "$source.input1_2bit.fields.path"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	546 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	547 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	548
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	549 <xml name="effectiveGenomeSize">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	550 <conditional name="effectiveGenomeSize">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	551 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	552 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	553 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	554 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	555 <option value="93260000">ce10 (93260000)</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	556 <option value="121400000">dm3 (121400000)</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	557 <option value="2451960000" selected="true">hg19 (2451960000)</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	558 <option value="2150570000">mm9 (2150570000)</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	559 <option value="specific">user specified</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	560 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	561 <when value="specific">
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	562 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	563 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	564 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	565 <when value="2150570000" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	566 <when value="2451960000" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	567 <when value="121400000" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	568 <when value="93260000" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	569 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	570 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	571
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	572 <xml name="skipNAs">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	573 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	574 label="Ignore missing data?"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	575 help="This parameter determines if non-covered regions
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	576 (regions without overlapping reads) in a bam/bigWig file
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	577 should be skipped. The default is to treat those
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	578 regions as having a value of zero. The decision to
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	579 skip non-covered regions depends on the interpretation
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	580 of the data. Non-covered regions may represent, for
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	581 example, repetitive regions that should be ignored.
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	582 (default: False)" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	583 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	584
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	585 <xml name="input_save_matrix_values">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	586 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	587 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	588
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	589 <xml name="input_graphic_output_settings">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	590 <conditional name="output" >
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	591 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	592 <option value="no" selected="true">no</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	593 <option value="yes">yes</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	594 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	595 <when value="no" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	596 <when value="yes">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	597 <yield />
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	598 <param name="saveSortedRegions" type="boolean"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	599 label="Save the regions after skipping zeros or min/max threshold values"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	600 help="The order of the regions in the file follows the sorting order selected. This is useful,
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	601 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	602 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	603 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	604 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	605
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	606
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	607 <xml name="input_image_file_format">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	608 <param argument="--outFileFormat" type="select" label="Image file format">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	609 <option value="png" selected="true">png</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	610 <option value="pdf">pdf</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	611 <option value="svg">svg</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	612 <option value="eps">eps</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	613 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	614 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	615
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	616 <xml name="output_dpi">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	617 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	618 label="Image dpi" help=""/>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	619 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	620
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	621 <xml name="output_image_file_format">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	622 <data format="png" name="outFileName" label="${tool.name} image">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	623 <change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	624 <when input="output.outFileFormat" value="pdf" format="pdf" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	625 <when input="output.outFileFormat" value="svg" format="svg" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	626 <when input="output.outFileFormat" value="eps" format="eps" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	627 </change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	628 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	629 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	630
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	631 <xml name="output_image_file_format_not_nested">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	632 <data format="png" name="outFileName" label="${tool.name} image">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	633 <change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	634 <when input="outFileFormat" value="pdf" format="pdf" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	635 <when input="outFileFormat" value="svg" format="svg" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	636 <when input="outFileFormat" value="eps" format="eps" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	637 </change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	638 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	639 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	640
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	641 <xml name="output_save_matrix_values">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	642 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	643 <filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	644 ((
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	645 output['showOutputSettings'] == 'yes' and
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	646 output['saveMatrix'] is True
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	647 ))
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	648 </filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	649 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	650 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	651
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	652 <xml name="output_graphic_outputs">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	653 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	654 <filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	655 ((
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	656 output['showOutputSettings'] == 'yes' and
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	657 output['saveSortedRegions'] is True
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	658 ))
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	659 </filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	660 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	661 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	662
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	663 <xml name="colorMap">
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	664 <param name="colorMap" type="select" label="Color map to use for the heatmap"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	665 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	666 multiple="true">
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	667 <option value="RdYlBu" selected="true">RdYlBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	668 <option value="Accent">Accent</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	669 <option value="Spectral">Spectral</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	670 <option value="Set1">Set1</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	671 <option value="Set2">Set2</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	672 <option value="Set3">Set3</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	673 <option value="Dark2">Dark2</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	674 <option value="Reds">Reds</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	675 <option value="Oranges">Oranges</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	676 <option value="Greens">Greens</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	677 <option value="Blues">Blues</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	678 <option value="Greys">Greys</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	679 <option value="Purples">Purples</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	680 <option value="Paired">Paired</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	681 <option value="Pastel1">Pastel1</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	682 <option value="Pastel2">Pastel2</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	683 <option value="spring">spring</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	684 <option value="summer">summer</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	685 <option value="autumn">autumn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	686 <option value="winter">winter</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	687 <option value="hot">hot</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	688 <option value="coolwarm">coolwarm</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	689 <option value="cool">cool</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	690 <option value="seismic">seismic</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	691 <option value="terrain">terrain</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	692 <option value="ocean">ocean</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	693 <option value="rainbow">rainbow</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	694 <option value="bone">bone</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	695 <option value="flag">flag</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	696 <option value="prism">prism</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	697 <option value="cubehelix">cubehelix</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	698 <option value="binary">binary</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	699 <option value="pink">pink</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	700 <option value="gray">gray</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	701 <option value="copper">copper</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	702 <option value="BrBG">BrBG</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	703 <option value="BuGn">BuGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	704 <option value="BuPu">BuPu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	705 <option value="GnBu">GnBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	706 <option value="OrRd">OrRd</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	707 <option value="PiYG">PiYG</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	708 <option value="PRGn">PRGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	709 <option value="PuOr">PuOr</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	710 <option value="PuRd">PuRd</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	711 <option value="PuBu">PuBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	712 <option value="RdBu">RdBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	713 <option value="RdGy">RdGy</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	714 <option value="RdPu">RdPu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	715 <option value="YlGn">YlGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	716 <option value="PuBuGn">PuBuGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	717 <option value="RdYlGn">RdYlGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	718 <option value="YlGnBu">YlGnBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	719 <option value="YlOrBr">YlOrBr</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	720 <option value="YlOrRd">YlOrRd</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	721 <option value="gist_gray">gist_gray</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	722 <option value="gist_stern">gist_stern</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	723 <option value="gist_earth">gist_earth</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	724 <option value="gist_yarg">gist_yarg</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	725 <option value="gist_ncar">gist_ncar</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	726 <option value="gist_rainbow">gist_rainbow</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	727 <option value="gist_heat">gist_heat</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	728 <option value="gnuplot">gnuplot</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	729 <option value="gnuplot2">gnuplot2</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	730 <option value="CMRmap">CMRmap</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	731 <option value="bwr">bwr</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	732 <option value="hsv">hsv</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	733 <option value="brg">brg</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	734 <option value="jet">jet</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	735 <option value="afmhot">afmhot</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	736 <option value="Accent_r">Accent reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	737 <option value="Spectral_r">Spectral reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	738 <option value="Set1_r">Set1 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	739 <option value="Set2_r">Set2 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	740 <option value="Set3_r">Set3 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	741 <option value="Dark2_r">Dark2 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	742 <option value="Reds_r">Reds reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	743 <option value="Oranges_r">Oranges reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	744 <option value="Greens_r">Greens reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	745 <option value="Blues_r">Blues reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	746 <option value="Greys_r">Greys reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	747 <option value="Purples_r">Purples reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	748 <option value="Paired_r">Paired reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	749 <option value="Pastel1_r">Pastel1 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	750 <option value="Pastel2_r">Pastel2 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	751 <option value="spring_r">spring reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	752 <option value="summer_r">summer reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	753 <option value="autumn_r">autumn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	754 <option value="winter_r">winter reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	755 <option value="hot_r">hot reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	756 <option value="coolwarm_r">coolwarm reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	757 <option value="cool_r">cool reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	758 <option value="seismic_r">seismic reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	759 <option value="terrain_r">terrain reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	760 <option value="ocean_r">ocean reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	761 <option value="rainbow_r">rainbow reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	762 <option value="bone_r">bone reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	763 <option value="flag_r">flag reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	764 <option value="prism_r">prism reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	765 <option value="cubehelix_r">cubehelix reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	766 <option value="binary_r">binary reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	767 <option value="pink_r">pink reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	768 <option value="gray_r">gray reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	769 <option value="copper_r">copper reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	770 <option value="BrBG_r">BrBG reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	771 <option value="BuGn_r">BuGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	772 <option value="BuPu_r">BuPu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	773 <option value="GnBu_r">GnBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	774 <option value="OrRd_r">OrRd reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	775 <option value="PiYG_r">PiYG reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	776 <option value="PRGn_r">PRGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	777 <option value="PuOr_r">PuOr reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	778 <option value="PuRd_r">PuRd reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	779 <option value="PuBu_r">PuBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	780 <option value="RdBu_r">RdBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	781 <option value="RdGy_r">RdGy reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	782 <option value="RdPu_r">RdPu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	783 <option value="YlGn_r">YlGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	784 <option value="PuBuGn_r">PuBuGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	785 <option value="RdYlBu_r">RdYlBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	786 <option value="RdYlGn_r">RdYlGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	787 <option value="YlGnBu_r">YlGnBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	788 <option value="YlOrBr_r">YlOrBr reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	789 <option value="YlOrRd_r">YlOrRd reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	790 <option value="gist_gray_r">gist_gray reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	791 <option value="gist_stern_r">gist_stern reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	792 <option value="gist_earth_r">gist_earth reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	793 <option value="gist_yarg_r">gist_yarg reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	794 <option value="gist_ncar_r">gist_ncar reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	795 <option value="gist_rainbow_r">gist_rainbow reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	796 <option value="gist_heat_r">gist_heat reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	797 <option value="gnuplot_r">gnuplot reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	798 <option value="gnuplot2_r">gnuplot2 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	799 <option value="CMRmap_r">CMRmap reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	800 <option value="bwr_r">bwr reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	801 <option value="hsv_r">hsv reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	802 <option value="brg_r">brg reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	803 <option value="jet_r">jet reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	804 <option value="afmhot_r">afmhot reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	805 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	806
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	807 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	808
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	809 </macros>

Mercurial > repos > bgruening > deeptools_multi_bam_summary

annotate deepTools_macros.xml @ 19:c7ac0b77d00a draft