deeptools_multi_bam_summary: deepTools

annotate deepTools_macros.xml @ 30:f0287980cc20 draft

"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97"

author	bgruening
date	Fri, 11 Feb 2022 09:58:36 +0000
parents	4bd8dfe714c2
children	d9e59cf2fdf6

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>
30 f0287980cc20 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97" bgruening parents: 29 diff changeset	4 <token name="@WRAPPER_VERSION@">3.5.1.0</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>
30 f0287980cc20 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97" bgruening parents: 29 diff changeset	7 <requirement type="package" version="3.5.1">deeptools</requirement>
26 a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	8 <requirement type="package" version="1.9">samtools</requirement>
16 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"
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	103 help="If set, then regions with zero counts for all BAM/CRAM files are included. The default behavior is to ignore such regions." />
0 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=":"/>
24 0c5507cd1617 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 23 diff changeset	121 <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	122 </valid>
3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	123 </sanitizer>
3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	124 </param>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	125 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	126
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	127 <xml name="smoothLength">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	128 <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	129 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	130 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	131 </xml>
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
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	134 <xml name="kmeans_clustering">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	135 <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	136 <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	137 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	138 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	139 <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	140 <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	141 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	142 <when value="no">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	143 <conditional name="clustering">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	144 <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	145 <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	146 <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	147 <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	148 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	149 <when value="kmeans">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	150 <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	151 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	152 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	153 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	154 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	155 </when>
2 46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	156 <when value="hclust">
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	157 <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	158 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	159 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	160 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	161 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	162 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	163 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	164 </when>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	165 <when value="none" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	166 </conditional>
29 4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	167 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	168 label="Compute the silhouette score for each region"
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	169 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	170 The silhouette score is a measure of how similar a region is to other regions in the same cluster as
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	171 opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	172 The silhouette evaluation can be very slow when you have more than 100 000 regions." />
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	173 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	174 <when value="yes" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	175 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	176 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	177
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	178 <token name="@KMEANS_CLUSTERING@">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	179 #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	180 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	181 #if int($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	182 --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	183 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	184 #end if
2 46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	185 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	186 #if int($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	187 --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	188 #end if
46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	189 #end if
29 4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	190 $advancedOpt.used_multiple_regions.silhouette
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	191 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	192 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	193
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	194 <xml name="samFlags">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	195 <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	196 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	197 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	198 <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	199 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	200 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	201 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	202
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	203 <xml name="fragLength">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	204 <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	205 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	206 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	207 <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	208 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	209 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	210 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	211
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	212 <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	213 <expand macro="extendReads" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	214 <expand macro="ignoreDuplicates" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	215 <expand macro="centerReads" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	216 <expand macro="minMappingQuality" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	217 <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	218 <expand macro="fragLength" />
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	219 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	220
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	221 <xml name="gtf_options">
21 955d91e713d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c bgruening parents: 19 diff changeset	222 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	223 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	224 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	225 <param argument="--transcriptID" optional="True" value="transcript" type="text"
25 89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	226 label="transcript designator"
29 4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	227 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	228 <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	229 label="exon designator"
29 4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	230 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	231 <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	232 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	233 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	234 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	235 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	236 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	237 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	238
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	239
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	240 <xml name="plotNumbers">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	241 <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	242 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	243 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	244 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	245
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	246 <xml name="extendReads">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	247 <conditional name="doExtendCustom">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	248 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	249 help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	250 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	251 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	252 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	253 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	254 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	255 <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	256 <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	257 <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	258 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	259 <when value="no" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	260 <when value="yes" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	261 <when value="custom">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	262 <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	263 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	264 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	265 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	266 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	267 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	268
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	269 <xml name="corMethod">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	270 <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	271 <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	272 <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	273 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	274 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	275
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	276 <xml name="distanceBetweenBins">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	277 <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	278 label="Distance between bins"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	279 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	280 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	281 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	282 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	283 considered."/>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	284 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	285
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	286 <xml name="centerReads">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	287 <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	288 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	289 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	290 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	291
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	292 <xml name="ignoreDuplicates">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	293 <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	294 label="Ignore duplicates"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	295 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	296 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	297
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	298 <xml name="sortUsing">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	299 <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	300 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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	308 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	309
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	310 <xml name="sortRegionsComputeMatrix">
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	311 <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	312 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	313 <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	314 <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	315 <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	316 <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	317 </param>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	318 </xml>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	319
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	320 <xml name="sortRegions">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	321 <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	322 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	323 <option value="no">maintain the same ordering as the input files</option>
15 ef0cc90a66b8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 14 diff changeset	324 <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	325 <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	326 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	327 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	328
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	329 <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	330 <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	331 label="Minimum mapping quality"
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	332 help= "If set, only reads with a mapping quality score at least this high are considered."/>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	333 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	334
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	335 <xml name="skipZeros">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	336 <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	337 label ="Skip zeros"
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	338 help ="If set, then zero counts that happen for all BAM/CRAM files given are ignored. This may result in fewer considered regions." />
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	339 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	340
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	341 <xml name="fragmentLength">
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	342 <param argument="--fragmentLength" type="integer" min="1" optional="true"
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	343 label="Fragment length used for the sequencing"
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	344 help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	345 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	346
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	347 <xml name="scaleFactor">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	348 <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	349 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	350 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	351
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	352 <xml name="scaleFactors">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	353 <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	354 <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	355 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	356
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	357 <xml name="stdio">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	358 <stdio>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	359 <exit_code range="1:" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	360 <exit_code range=":-1" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	361 <regex match="Error:" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	362 <regex match="Exception:" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	363 <regex match="EXception:" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	364 <regex match="Traceback" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	365 </stdio>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	366 </xml>
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 <xml name="pseudocount">
26 a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	369 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	370 </xml>
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 <token name="@REFERENCES@">
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 .. class:: infomark
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	375
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	376 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	377
29 4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	378 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	379
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	380 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	381
29 4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	382 .. _Biostars: http://biostars.org
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	383 .. _on github: http://github.com
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	384 .. _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	385 .. _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	386 .. _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	387
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	388 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	389 <xml name="citations">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	390 <citations>
8 3c94b764e274 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 7 diff changeset	391 <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	392 <yield />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	393 </citations>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	394 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	395
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	396 <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	397 <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	398 <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	399 <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	400 <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	401 </param>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	402 <when value="No">
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	403 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	404 label="BAM/CRAM file" multiple="true"
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	405 help=""/>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	406 </when>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	407 <when value="Yes">
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	408 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	409 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	410 </repeat>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	411 </when>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	412 </conditional>
3 41c2e05aa70c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 2 diff changeset	413 </xml>
41c2e05aa70c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 2 diff changeset	414
18 50da5a8ab41d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 16 diff changeset	415 <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	416 <conditional name="multibigwig_conditional">
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	417 <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
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	418 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	419 <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	420 <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	421 </param>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	422 <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	423 <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	424 label="@LABEL@"
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	425 help="You can generate a bigWig file from a BAM/CRAM 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	426 </when>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	427 <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	428 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	429 <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM 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	430 </repeat>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	431 </when>
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	432 </conditional>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	433 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	434
26 a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	435 <xml name="custom_sample_labels">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	436 <conditional name="custom_sample_labels_conditional">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	437 <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	438 <option value="No" selected="true">No, use sample names in the history</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	439 <option value="Yes">Yes, I want to specify new labels</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	440 </param>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	441 <when value="No">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	442 </when>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	443 <when value="Yes">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	444 <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., "sample 1" "sample 2")">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	445 <sanitizer>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	446 <valid initial="string.printable">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	447 </valid>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	448 </sanitizer>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	449 </param>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	450 </when>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	451 </conditional>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	452 </xml>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	453
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	454 <xml name="plotTitle">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	455 <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	456 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	457 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	458 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	459
26 a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	460 <xml name="legendLocation">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	461 <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	462 <option value="best" selected="true">Best (automatic)</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	463 <option value="upper-right">upper-right</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	464 <option value="upper-left">upper-left</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	465 <option value="upper-center">upper-center</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	466 <option value="lower-right">lower-right</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	467 <option value="lower-left">lower-left</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	468 <option value="lower-center">lower-center</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	469 <option value="center-right">center-right</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	470 <option value="center-left">center-left</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	471 <option value="center">center</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	472 <option value="none">none (only works for heatmaps</option>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	473 </param>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	474 </xml>
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	475
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	476 <xml name="labelRotation">
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	477 <param argument="--labelRotation" type="integer" value="0"
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	478 label="Rotation of the X-axis labels (in degrees)"
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	479 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	480 </xml>
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	481
2 46909e251980 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 1 diff changeset	482
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	483 <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	484 <![CDATA[
26 a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	486 #set custom_labels=labels
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	487 #end if
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	488 #set files=[]
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	489 #set labels=[]
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	490 #import re
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	491 #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	492 #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	493 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
24 0c5507cd1617 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 23 diff changeset	494 ln -s '${bamfile}' './${counter}.bam' &&
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	495 #if $bamfile.ext == 'bam':
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	497 #else:
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	499 #end if
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	500 #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	501 #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	502 #end for
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	503 #else:
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	504 #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	505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
24 0c5507cd1617 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 23 diff changeset	506 ln -s '${f.bamfiles}' './${counter}.bam' &&
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	507 #if $f.bamfiles.ext == 'bam':
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	508 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	509 #else:
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	510 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	511 #end if
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	512 #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	513 #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	514 #end for
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	515 #end if
26 a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	516 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	517 #set labels=custom_labels
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	518 #end if
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	519 ]]>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	520 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	521
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	522 <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	523 <![CDATA[
27 24556753d171 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 26 diff changeset	524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
26 a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	525 #set custom_labels=labels
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	526 #end if
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	527 #set files=[]
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	528 #set labels=[]
16 d53a44a6cc72 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 15 diff changeset	529 #import re
14 cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	530 #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	531 #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	532 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
24 0c5507cd1617 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 23 diff changeset	533 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	534 #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	535 #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	536 #end for
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	537 #else:
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	538 #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	539 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
24 0c5507cd1617 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 23 diff changeset	540 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	541 #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	542 #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	543 #end for
cd485e0524c2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 13 diff changeset	544 #end if
27 24556753d171 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 26 diff changeset	545 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
26 a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	546 #set labels=custom_labels
a1a84914d00d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 25 diff changeset	547 #end if
0 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 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	550
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	551 <xml name="blacklist">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	552 <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	553 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	554 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	555 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	556
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	557 <token name="@blacklist@">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	558 <![CDATA[
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	559 #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	560 #set blfiles=[]
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	561 #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	562 #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	563 #end for
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	564 #if $blfiles != ["'None'"]:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	565 --blackListFileName #echo ' '.join($blfiles)#
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	566 #end if
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	567 #end if
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	568 ]]>
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	569 </token>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	570
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	571 <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	572 <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	573 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	574 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	575 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	576
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	577 <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	578 <![CDATA[
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	579 #set files=[]
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	580 #set labels=[]
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	581 #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	582 #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	583 #silent $labels.append("'%s'" % $f.display_name)
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	584 #end for
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	585 #if len($files) > 0:
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	586 --BED #echo ' '.join($files)#
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	587 --regionLabels #echo ' '.join($labels)#
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	588 #end if
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	589 ]]>
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	590 </token>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	591
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	592 <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	593 <conditional name="source">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	594 <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	595 <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	596 <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	597 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	598 <when value="cached">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	599 <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	600 <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	601 <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	602 <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	603 </options>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	604 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	605 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	606 <when value="history">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	607 <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	608 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	609 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	610 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	611
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	612 <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	613 #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	614 --genome $source.input1
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	615 #else:
24 0c5507cd1617 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 23 diff changeset	616 --genome '$source.input1_2bit.fields.path'
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	617 #end if
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	618 </token>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	619
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	620 <xml name="effectiveGenomeSize">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	621 <conditional name="effectiveGenomeSize">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	622 <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	623 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	624 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	625 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	626 <option value="93260000">ce10 (93260000)</option>
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	627 <option value="130428560">dm3 (130428560)</option>
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	628 <option value="125464728">dm6 (125464728)</option>
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	629 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	630 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	631 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	632 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	633 <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	634 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	635 <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	636 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	637 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	638 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	639 <when value="93260000" />
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	640 <when value="130428560" />
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	641 <when value="125464728" />
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	642 <when value="2685511504" />
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	643 <when value="2701495761" />
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	644 <when value="2304947926" />
ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	645 <when value="2308125349" />
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	646 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	647 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	648
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	649 <xml name="skipNAs">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	650 <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	651 label="Ignore missing data?"
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	652 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	653 (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	654 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	655 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	656 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	657 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	658 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	659 (default: False)" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	660 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	661
28 04b8cf97e6e0 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 27 diff changeset	662 <xml name="skipZeroOverZero">
04b8cf97e6e0 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 27 diff changeset	663 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
04b8cf97e6e0 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 27 diff changeset	664 help="Skip bins where BOTH files lack coverage.">
04b8cf97e6e0 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 27 diff changeset	665 <option value="" selected="true">No</option>
04b8cf97e6e0 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 27 diff changeset	666 <option value="--skipZeroOverZero">Yes, skip them.</option>
04b8cf97e6e0 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 27 diff changeset	667 </param>
04b8cf97e6e0 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 27 diff changeset	668 </xml>
04b8cf97e6e0 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 27 diff changeset	669
25 89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	670 <xml name="exactScaling">
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	671 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	672 label="Compute an exact scaling factor"
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	673 help="Compute an exact scaling factor rather than one based on
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	674 sampled reads. This is only useful in cases where you are
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	675 filtering some alignments out AND this are both rare and
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	676 tend to clump together in the genome. In such cases the
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	677 region-based sampling employed by deepTools would produce
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	678 inaccurate scaling factors. Note that this option results
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	679 in the process taking significantly more time to complete." />
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	680 </xml>
89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	681
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	682 <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	683 <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	684 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	685
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	686 <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	687 <conditional name="output" >
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	688 <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	689 <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	690 <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	691 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	692 <when value="no" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	693 <when value="yes">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	694 <yield />
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	695 <param name="saveSortedRegions" type="boolean"
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	696 argument="--outFileSortedRegions"
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	697 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	698 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	699 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	700 </when>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	701 </conditional>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	702 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	703
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	704
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	705 <xml name="input_image_file_format">
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	706 <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	707 <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	708 <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	709 <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	710 <option value="eps">eps</option>
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	711 <option value="plotly">plotly</option>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	712 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	713 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	714
10 024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	715 <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	716 <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	717 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	718 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 9 diff changeset	719
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	720 <xml name="output_image_file_format">
25 89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	721 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	722 <change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	723 <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	724 <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	725 <when input="output.outFileFormat" value="eps" format="eps" />
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	726 <when input="output.outFileFormat" value="plotly" format="html" />
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	727 </change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	728 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	729 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	730
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	731 <xml name="output_image_file_format_not_nested">
25 89c5b63a954d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 24 diff changeset	732 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	733 <change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	734 <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	735 <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	736 <when input="outFileFormat" value="eps" format="eps" />
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	737 <when input="outFileFormat" value="plotly" format="html" />
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	738 </change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	739 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	740 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	741
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	742 <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	743 <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	744 <filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	745 ((
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	746 output['showOutputSettings'] == 'yes' and
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	747 output['saveMatrix'] is True
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	748 ))
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	749 </filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	750 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	751 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	752
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	753 <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	754 <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	755 <filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	756 ((
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	757 output['showOutputSettings'] == 'yes' and
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	758 output['saveSortedRegions'] is True
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	759 ))
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	760 </filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	761 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	762 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	763
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	764 <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	765 <param name="colorMap" type="select" label="Color map to use for the heatmap"
22 ebc070a847a4 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 21 diff changeset	766 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	767 <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	768 <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	769 <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	770 <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	771 <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	772 <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	773 <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	774 <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	775 <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	776 <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	777 <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	778 <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	779 <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	780 <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	781 <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	782 <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	783 <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	784 <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	785 <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	786 <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	787 <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	788 <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	789 <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	790 <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	791 <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	792 <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	793 <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	794 <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	795 <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	796 <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	797 <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	798 <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	799 <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	800 <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	801 <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	802 <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	803 <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	804 <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	805 <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	806 <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	807 <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	808 <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	809 <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	810 <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	811 <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	812 <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	813 <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	814 <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	815 <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	816 <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	817 <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	818 <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	819 <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	820 <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	821 <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	822 <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	823 <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	824 <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	825 <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	826 <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	827 <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	828 <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	829 <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	830 <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	831 <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	832 <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	833 <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	834 <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	835 <option value="afmhot">afmhot</option>
29 4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	836 <option value="Wistia">Wistia</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	837 <option value="cividis">cividis</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	838 <option value="icefire">icefire</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	839 <option value="inferno">inferno</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	840 <option value="magma">magma</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	841 <option value="mako">mako</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	842 <option value="nipy_spectral">nipy_spectral</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	843 <option value="plasma">plasma</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	844 <option value="rocket">rocket</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	845 <option value="tab10">tab10</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	846 <option value="tab20">tab20</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	847 <option value="tab20b">tab20b</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	848 <option value="tab20c">tab20c</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	849 <option value="twilight">twilight</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	850 <option value="twilight_shifted">twilight_shifted</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	851 <option value="viridis">viridis</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	852 <option value="vlag">vlag</option>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	853 <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	854 <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	855 <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	856 <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	857 <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	858 <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	859 <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	860 <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	861 <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	862 <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	863 <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	864 <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	865 <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	866 <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	867 <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	868 <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	869 <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	870 <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	871 <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	872 <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	873 <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	874 <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	875 <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	876 <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	877 <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	878 <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	879 <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	880 <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	881 <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	882 <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	883 <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	884 <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	885 <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	886 <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	887 <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	888 <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	889 <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	890 <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	891 <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	892 <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	893 <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	894 <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	895 <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	896 <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	897 <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	898 <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	899 <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	900 <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	901 <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	902 <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	903 <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	904 <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	905 <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	906 <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	907 <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	908 <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	909 <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	910 <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	911 <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	912 <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	913 <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	914 <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	915 <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	916 <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	917 <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	918 <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	919 <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	920 <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	921 <option value="afmhot_r">afmhot reversed</option>
29 4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	922 <option value="Wistia_r">Wistia reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	923 <option value="cividis_r">cividis reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	924 <option value="icefire_r">icefire reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	925 <option value="inferno_r">inferno reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	926 <option value="magma_r">magma reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	927 <option value="mako_r">mako reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	928 <option value="nipy_spectral_r">nipy_spectral reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	929 <option value="plasma_r">plasma reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	930 <option value="rocket_r">rocket reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	931 <option value="tab10_r">tab10 reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	932 <option value="tab20_r">tab20 reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	933 <option value="tab20b_r">tab20b reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	934 <option value="tab20c_r">tab20c reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	935 <option value="twilight_r">twilight reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	936 <option value="twilight_shifted_r">twilight_shifted reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	937 <option value="viridis_r">viridis reversed</option>
4bd8dfe714c2 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 28 diff changeset	938 <option value="vlag_r">vlag reversed</option>
0 812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	939 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	940
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	941 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	942
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: diff changeset	943 </macros>

Mercurial > repos > bgruening > deeptools_multi_bam_summary

annotate deepTools_macros.xml @ 30:f0287980cc20 draft