deeptools_plot_enrichment: deepTools

annotate deepTools_macros.xml @ 21:d95486ad55e8 draft default tip

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9

author	bgruening
date	Thu, 01 Jun 2023 09:59:47 +0000
parents	c2e104f4322d
children

rev	line source
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	1 <macros>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	2
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
21 d95486ad55e8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 20 diff changeset	4 <token name="@TOOL_VERSION@">3.5.2</token>
d95486ad55e8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 20 diff changeset	5 <token name="@GALAXY_VERSION@">20.01</token>
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	6 <xml name="requirements">
f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	7 <requirements>
21 d95486ad55e8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 20 diff changeset	8 <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	9 <requirement type="package" version="1.9">samtools</requirement>
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	10 </requirements>
f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	11 <expand macro="stdio" />
f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	12 <version_command>@BINARY@ --version</version_command>
f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	13 </xml>
f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	14
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	15 <xml name="advancedOpt_scaffold">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	16 <conditional name="advancedOpt">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	17 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	18 <option value="no" selected="true">no</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	19 <option value="yes">yes</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	20 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	21 <when value="no" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	22 <when value="yes">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	23 <yield/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	24 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	25 </conditional>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	26 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	27
8 f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	28 <token name="@PLOTWIDTHHEIGHT@">
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	29 --plotWidth '$advancedOpt.plotWidth'
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	30 --plotHeight '$advancedOpt.plotHeight'
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	31 </token>
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	32
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	33 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	34 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	35 label="Plot height"
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	36 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	37
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	38 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	39 label="Plot width"
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	40 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	41 </xml>
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	42
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	43 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	44 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	45 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	46 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	47 --extendReads
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	48 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	49 $advancedOpt.ignoreDuplicates
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	50 $advancedOpt.centerReads
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	51 #if $advancedOpt.minMappingQuality:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	52 --minMappingQuality '$advancedOpt.minMappingQuality'
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	53 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	54 #if $advancedOpt.samFlagInclude:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	55 --samFlagInclude $advancedOpt.samFlagInclude
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	56 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	57 #if $advancedOpt.samFlagExclude:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	58 --samFlagExclude $advancedOpt.samFlagExclude
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	59 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	60 #if $advancedOpt.minFragmentLength:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	61 --minFragmentLength $advancedOpt.minFragmentLength
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	62 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	63 #if $advancedOpt.maxFragmentLength:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	64 --maxFragmentLength $advancedOpt.maxFragmentLength
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	65 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	66 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	67
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	68 <token name="@ADVANCED_OPTS_GTF@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	69 $advancedOpt.metagene
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	70 #if $advancedOpt.transcriptID:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	71 --transcriptID $advancedOpt.transcriptID
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	72 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	73 #if $advancedOpt.exonID:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	74 --exonID $advancedOpt.exonID
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	75 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	76 #if $advancedOpt.transcript_id_designator:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	77 --transcript_id_designator $advancedOpt.transcript_id_designator
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	78 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	79 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	80
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	81 <xml name="heatmap_options">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	82 <expand macro="zMin_zMax" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	83 <expand macro="colorMap" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	84 <expand macro="plotTitle" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	85 <expand macro="plotNumbers" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	86 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	87
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	88 <token name="@HEATMAP_OPTIONS@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	89 #if str($plotting_type.zMin) != "":
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	90 --zMin $plotting_type.zMin
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	91 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	92 #if str($plotting_type.zMax) != "":
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	93 --zMax $plotting_type.zMax
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	94 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	95 --colorMap '$plotting_type.colorMap'
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	96 $plotting_type.plotNumbers
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	97 --plotTitle '$plotting_type.plotTitle'
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	98 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	99
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	100
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	101 <xml name="includeZeros">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	102 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	103 label="Include zeros"
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	104 help="If set, then regions with zero counts for all BAM/CRAM files are included. The default behavior is to ignore such regions." />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	105 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	106
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	107 <xml name="zMin_zMax">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	108 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	109 help="If not specified the value is set automatically."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	110 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	111 help="If not specified the value is set automatically."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	112 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	113
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	114 <xml name="region_limit_operation">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	115 <param argument="--region" type="text" value=""
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	116 label="Region of the genome to limit the operation to"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	117 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".">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	118 <sanitizer>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	119 <valid initial="string.letters,string.digits">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	120 <add value="\|"/>
2 d1d773ef645d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 1 diff changeset	121 <add value=":"/>
14 e0be6dd1b738 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 13 diff changeset	122 <add value="."/>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	123 </valid>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	124 </sanitizer>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	125 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	126 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	127
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	128 <xml name="smoothLength">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	129 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	130 label="Smooth values using the following length (in bases)"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	131 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."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	132 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	133
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	134
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	135 <xml name="kmeans_clustering">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	136 <conditional name="used_multiple_regions">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	137 <param name="used_multiple_regions_options" type="select"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	138 label="Did you compute the matrix with more than one groups of regions?"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	139 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.">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	140 <option value="yes">Yes, I used multiple groups of regions</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	141 <option value="no">No, I used only one group</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	142 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	143 <when value="no">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	144 <conditional name="clustering">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	145 <param name="clustering_options" type="select" label="Clustering algorithm">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	146 <option value="none">No clustering</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	147 <option value="kmeans">Kmeans clustering</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	148 <option value="hclust">Hierarchical clustering</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	149 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	150 <when value="kmeans">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	151 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	152 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	153 This only works for data that is not grouped, otherwise only the first group will be clustered.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	154 If more specific clustering methods are required it is advisable to save the underlying matrix and
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	155 run the clustering using other software."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	156 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	157 <when value="hclust">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	158 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	159 help="WARNING: This option causes the tool to run for a very long time! When this option is
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	160 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	161 This only works for data that is not grouped, otherwise only the first group will be clustered.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	162 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	163 If more specific clustering methods are required it is advisable to save the underlying matrix and
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	164 run the clustering using other software."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	165 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	166 <when value="none" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	167 </conditional>
19 057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	168 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	169 label="Compute the silhouette score for each region"
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	170 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	171 The silhouette score is a measure of how similar a region is to other regions in the same cluster as
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	172 opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	173 The silhouette evaluation can be very slow when you have more than 100 000 regions." />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	174 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	175 <when value="yes" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	176 </conditional>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	177 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	178
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	179 <token name="@KMEANS_CLUSTERING@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	180 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	181 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	182 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	183 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	184 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	185 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	186 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	187 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	188 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	189 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	190 #end if
19 057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	191 $advancedOpt.used_multiple_regions.silhouette
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	192 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	193 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	194
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	195 <xml name="samFlags">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	196 <param argument="--samFlagInclude" type="integer" optional="True" value=""
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	197 label="Include reads based on the SAM flag"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	198 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."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	199 <param argument="--samFlagExclude" type="integer" optional="True" value=""
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	200 label="Exclude reads based on the SAM flag"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	201 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."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	202 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	203
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	204 <xml name="fragLength">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	205 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	206 label="Minimum fragment length for inclusion."
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	207 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	208 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	209 label="Maximum fragment length for inclusion."
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	210 help="A value of 0 (the default) is equivalent to no maximum." />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	211 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	212
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	213 <xml name="read_processing_options">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	214 <expand macro="extendReads" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	215 <expand macro="ignoreDuplicates" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	216 <expand macro="centerReads" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	217 <expand macro="minMappingQuality" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	218 <expand macro="samFlags" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	219 <expand macro="fragLength" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	220 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	221
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	222 <xml name="gtf_options">
11 94b1e196492d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c bgruening parents: 9 diff changeset	223 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	224 label="Use a metagene model"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	225 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." />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	226 <param argument="--transcriptID" optional="True" value="transcript" type="text"
15 67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	227 label="transcript designator"
19 057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	228 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" />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	229 <param argument="--exonID" optional="True" value="exon" type="text"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	230 label="exon designator"
19 057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	231 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" />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	232 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	233 label="transcriptID key designator"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	234 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	235 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	236 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	237 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	238 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	239
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	240
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	241 <xml name="plotNumbers">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	242 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	243 label="Plot the correlation value"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	244 help="If set, then the correlation number is plotted on top of the heatmap."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	245 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	246
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	247 <xml name="extendReads">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	248 <conditional name="doExtendCustom">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	249 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	250 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 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	251 By default each read mate is extended.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	252 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	253 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	254 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
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	255 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	256 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	257 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	258 <option value="custom">A custom length, which will be applied to ALL reads.</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	259 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	260 <when value="no" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	261 <when value="yes" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	262 <when value="custom">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	263 <param name="extendReadsValue" type="integer" value="300" min="1"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	264 label="Extend reads to the given average fragment size"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	265 help="Extend all reads to this length" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	266 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	267 </conditional>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	268 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	269
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	270 <xml name="corMethod">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	271 <param argument="--corMethod" type="select" label="Correlation method">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	272 <option value="spearman" selected="True">Spearman</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	273 <option value="pearson">Pearson</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	274 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	275 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	276
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	277 <xml name="distanceBetweenBins">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	278 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	279 label="Distance between bins"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	280 help="By default, multiBamSummary considers consecutive bins of
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	281 the specified 'Bin size'. However, to reduce the
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	282 computation time, a larger distance between bins can
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	283 be given. Larger distances result in fewer bins being
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	284 considered."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	285 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	286
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	287 <xml name="centerReads">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	288 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	289 label="Center regions with respect to the fragment length"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	290 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."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	291 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	292
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	293 <xml name="ignoreDuplicates">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	294 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	295 label="Ignore duplicates"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	296 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." />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	297 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	298
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	299 <xml name="sortUsing">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	300 <param argument="--sortUsing" type="select" label="Method used for sorting"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	301 help="For each row the method is computed.">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	302 <option value="mean" selected="true">mean</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	303 <option value="median">median</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	304 <option value="min">min</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	305 <option value="max">max</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	306 <option value="sum">sum</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	307 <option value="region_length">region length</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	308 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	309 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	310
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	311 <xml name="sortRegionsComputeMatrix">
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	312 <param argument="--sortRegions" type="select" label="Sort regions"
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	313 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	314 <option value="no">no ordering</option>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	315 <option value="keep" selected="true">maintain the same ordering as the input files</option>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	316 <option value="descend">descending order</option>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	317 <option value="ascend">ascending order</option>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	318 </param>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	319 </xml>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	320
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	321 <xml name="sortRegions">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	322 <param argument="--sortRegions" type="select" label="Sort regions"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	323 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	324 <option value="no">maintain the same ordering as the input files</option>
5 50efa005c0c6 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 4 diff changeset	325 <option value="descend" selected="true">descending order</option>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	326 <option value="ascend">ascending order</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	327 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	328 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	329
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	330 <xml name="minMappingQuality">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	331 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	332 label="Minimum mapping quality"
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	333 help= "If set, only reads with a mapping quality score at least this high are considered."/>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	334 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	335
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	336 <xml name="skipZeros">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	337 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	338 label ="Skip zeros"
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	339 help ="If set, then zero counts that happen for all BAM/CRAM files given are ignored. This may result in fewer considered regions." />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	340 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	341
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	342 <xml name="fragmentLength">
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	343 <param argument="--fragmentLength" type="integer" min="1" optional="true"
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	344 label="Fragment length used for the sequencing"
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	345 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 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	346 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	347
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	348 <xml name="scaleFactor">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	349 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	350 help="The computed scaling factor will be multiplied by this (default 1)." />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	351 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	352
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	353 <xml name="scaleFactors">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	354 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	355 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	356 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	357
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	358 <xml name="stdio">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	359 <stdio>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	360 <exit_code range="1:" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	361 <exit_code range=":-1" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	362 <regex match="Error:" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	363 <regex match="Exception:" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	364 <regex match="EXception:" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	365 <regex match="Traceback" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	366 </stdio>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	367 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	368
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	369 <xml name="pseudocount">
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	370 <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 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	371 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	372 <token name="@REFERENCES@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	373
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	374 .. class:: infomark
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	375
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	376 For more information on the tools, please visit our `help site`_.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	377
19 057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	378 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	379
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 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`_.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	381
19 057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	382 .. _Biostars: http://biostars.org
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	383 .. _on github: http://github.com
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	384 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	385 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	386 .. _help site: https://deeptools.readthedocs.org/
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	387
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	388 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	389 <xml name="citations">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	390 <citations>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	391 <citation type="doi">10.1093/nar/gkw257</citation>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	392 <yield />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	393 </citations>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	394 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	395
8 f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	396 <xml name="multiple_input_bams" tokens="MIN">
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	397 <conditional name="multibam_conditional">
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 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.">
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	399 <option value="No" selected="true">No</option>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	400 <option value="Yes">Yes</option>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	401 </param>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	402 <when value="No">
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	403 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	404 label="BAM/CRAM file" multiple="true"
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	405 help=""/>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	406 </when>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	407 <when value="Yes">
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	408 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	409 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	410 </repeat>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	411 </when>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	412 </conditional>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	413 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	414
8 f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	415 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	416 <conditional name="multibigwig_conditional">
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 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
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	418 is vital to you, select Yes below.">
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	419 <option value="No" selected="true">No</option>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	420 <option value="Yes">Yes</option>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	421 </param>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	422 <when value="No">
8 f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	423 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	424 label="@LABEL@"
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	425 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	426 </when>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	427 <when value="Yes">
8 f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	428 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 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."/>
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	430 </repeat>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	431 </when>
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	432 </conditional>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	433 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	434
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	435 <xml name="custom_sample_labels">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	436 <conditional name="custom_sample_labels_conditional">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 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.">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	438 <option value="No" selected="true">No, use sample names in the history</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	439 <option value="Yes">Yes, I want to specify new labels</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	440 </param>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	441 <when value="No">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	442 </when>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	443 <when value="Yes">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 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")">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	445 <sanitizer>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	446 <valid initial="string.printable">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	447 </valid>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	448 </sanitizer>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	449 </param>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	450 </when>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	451 </conditional>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	452 </xml>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	453
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	454 <xml name="plotTitle">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	455 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	456 label="Title of the plot"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	457 help="Title of the plot, to be printed on top of the generated image." />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	458 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	459
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	460 <xml name="legendLocation">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 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.">
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	462 <option value="best" selected="true">Best (automatic)</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	463 <option value="upper-right">upper-right</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	464 <option value="upper-left">upper-left</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	465 <option value="upper-center">upper-center</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	466 <option value="lower-right">lower-right</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	467 <option value="lower-left">lower-left</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	468 <option value="lower-center">lower-center</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	469 <option value="center-right">center-right</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	470 <option value="center-left">center-left</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	471 <option value="center">center</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	472 <option value="none">none (only works for heatmaps</option>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	473 </param>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	474 </xml>
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	475
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	476 <xml name="labelRotation">
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	477 <param argument="--labelRotation" type="integer" value="0"
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	478 label="Rotation of the X-axis labels (in degrees)"
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 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." />
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	480 </xml>
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	481
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	482
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	483 <token name="@multiple_input_bams@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	484 <![CDATA[
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
21 d95486ad55e8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 20 diff changeset	486 #set custom_labels=$custom_sample_labels_conditional.labels
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	487 #end if
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	488 #set files=[]
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	489 #set labels=[]
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	490 #import re
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	491 #if $multibam_conditional.orderMatters == "No":
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	492 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	493 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
14 e0be6dd1b738 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 13 diff changeset	494 ln -s '${bamfile}' './${counter}.bam' &&
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	495 #if $bamfile.ext == 'bam':
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	497 #else:
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	499 #end if
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	500 #silent $files.append("'%s.bam'" % $counter)
21 d95486ad55e8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 20 diff changeset	501 #silent $labels.append("'%s'" % $identifier)
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	502 #end for
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	503 #else:
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	504 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
14 e0be6dd1b738 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 13 diff changeset	506 ln -s '${f.bamfiles}' './${counter}.bam' &&
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	507 #if $f.bamfiles.ext == 'bam':
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	508 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	509 #else:
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	510 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	511 #end if
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	512 #silent $files.append("'%s.bam'" % $counter)
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	513 #silent $labels.append("'%s'" % $identifier)
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	514 #end for
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	515 #end if
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	516 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	517 #set labels=custom_labels
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	518 #end if
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	519 ]]>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	520 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	521
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	522 <token name="@multiple_input_bigwigs@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	523 <![CDATA[
17 c29ea378c294 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 16 diff changeset	524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
21 d95486ad55e8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 20 diff changeset	525 #set custom_labels=$custom_sample_labels_conditional.labels
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	526 #end if
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	527 #set files=[]
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	528 #set labels=[]
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	529 #import re
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	530 #if $multibigwig_conditional.orderMatters == "No":
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	531 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
8 f8b1d1ae388e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 6 diff changeset	532 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
14 e0be6dd1b738 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 13 diff changeset	533 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	534 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	535 #silent $labels.append("'%s'" % $identifier)
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	536 #end for
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	537 #else:
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	538 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	539 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
14 e0be6dd1b738 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 13 diff changeset	540 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	541 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
6 f3580352b9d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 5 diff changeset	542 #silent $labels.append("'%s'" % $identifier)
4 0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	543 #end for
0d41b2d92cfb planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 3 diff changeset	544 #end if
17 c29ea378c294 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 16 diff changeset	545 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
16 c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	546 #set labels=custom_labels
c8f8186a479a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 15 diff changeset	547 #end if
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	548 ]]>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	549 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	550
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	551 <xml name="blacklist">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	552 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	553 label="Blacklisted regions in BED/GTF format"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	554 help="One or more files containing regions to exclude from the analysis" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	555 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	556
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	557 <token name="@blacklist@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	558 <![CDATA[
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	559 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	560 #set blfiles=[]
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	561 #for $f in $advancedOpt.blackListFileName:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	562 #silent $blfiles.append("'%s'" % $f)
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	563 #end for
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	564 #if $blfiles != ["'None'"]:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	565 --blackListFileName #echo ' '.join($blfiles)#
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	566 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	567 #end if
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	568 ]]>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	569 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	570
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	571 <xml name="multiple_bed">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	572 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	573 label="Regions in BED/GTF format"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	574 help="One or more files containing regions to include in the analysis" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	575 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	576
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	577 <token name="@multiple_bed@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	578 <![CDATA[
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	579 #set files=[]
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	580 #set labels=[]
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	581 #for $f in $BED:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	582 #silent $files.append("'%s'" % $f)
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	583 #silent $labels.append("'%s'" % $f.display_name)
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	584 #end for
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	585 #if len($files) > 0:
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	586 --BED #echo ' '.join($files)#
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	587 --regionLabels #echo ' '.join($labels)#
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	588 #end if
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	589 ]]>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	590 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	591
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	592 <xml name="reference_genome_source">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	593 <conditional name="source">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	594 <param name="ref_source" type="select" label="Reference genome">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	595 <option value="cached">locally cached</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	596 <option value="history">in your history</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	597 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	598 <when value="cached">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 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">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	600 <options from_data_table="lastz_seqs">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	601 <filter type="sort_by" column="1" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	602 <validator type="no_options" message="No indexes are available." />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	603 </options>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	604 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	605 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	606 <when value="history">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	607 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	608 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	609 </conditional>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	610 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	611
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	612 <token name="@reference_genome_source@">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	613 #if $source.ref_source=="history":
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	614 --genome $source.input1
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	615 #else:
14 e0be6dd1b738 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 13 diff changeset	616 --genome '$source.input1_2bit.fields.path'
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	617 #end if
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	618 </token>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	619
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	620 <xml name="effectiveGenomeSize">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	621 <conditional name="effectiveGenomeSize">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	622 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 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.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 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.
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	625 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	626 <option value="93260000">ce10 (93260000)</option>
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	627 <option value="130428560">dm3 (130428560)</option>
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	628 <option value="125464728">dm6 (125464728)</option>
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	629 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	630 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	631 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	632 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	633 <option value="specific">user specified</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	634 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	635 <when value="specific">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	636 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	637 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	638 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	639 <when value="93260000" />
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	640 <when value="130428560" />
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	641 <when value="125464728" />
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	642 <when value="2685511504" />
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	643 <when value="2701495761" />
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	644 <when value="2304947926" />
4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	645 <when value="2308125349" />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	646 </conditional>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	647 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	648
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	649 <xml name="skipNAs">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	650 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	651 label="Ignore missing data?"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	652 help="This parameter determines if non-covered regions
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	653 (regions without overlapping reads) in a bam/bigWig file
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	654 should be skipped. The default is to treat those
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	655 regions as having a value of zero. The decision to
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	656 skip non-covered regions depends on the interpretation
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	657 of the data. Non-covered regions may represent, for
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	658 example, repetitive regions that should be ignored.
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	659 (default: False)" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	660 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	661
18 73c20192751d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 17 diff changeset	662 <xml name="skipZeroOverZero">
73c20192751d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 17 diff changeset	663 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
73c20192751d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 17 diff changeset	664 help="Skip bins where BOTH files lack coverage.">
73c20192751d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 17 diff changeset	665 <option value="" selected="true">No</option>
73c20192751d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 17 diff changeset	666 <option value="--skipZeroOverZero">Yes, skip them.</option>
73c20192751d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 17 diff changeset	667 </param>
73c20192751d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 17 diff changeset	668 </xml>
73c20192751d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 17 diff changeset	669
15 67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	670 <xml name="exactScaling">
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	671 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	672 label="Compute an exact scaling factor"
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	673 help="Compute an exact scaling factor rather than one based on
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	674 sampled reads. This is only useful in cases where you are
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	675 filtering some alignments out AND this are both rare and
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	676 tend to clump together in the genome. In such cases the
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	677 region-based sampling employed by deepTools would produce
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	678 inaccurate scaling factors. Note that this option results
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	679 in the process taking significantly more time to complete." />
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	680 </xml>
67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	681
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	682 <xml name="input_save_matrix_values">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	683 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	684 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	685
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	686 <xml name="input_graphic_output_settings">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	687 <conditional name="output" >
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	688 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	689 <option value="no" selected="true">no</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	690 <option value="yes">yes</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	691 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	692 <when value="no" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	693 <when value="yes">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	694 <yield />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	695 <param name="saveSortedRegions" type="boolean"
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	696 argument="--outFileSortedRegions"
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	697 label="Save the regions after skipping zeros or min/max threshold values"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	698 help="The order of the regions in the file follows the sorting order selected. This is useful,
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	699 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	700 </when>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	701 </conditional>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	702 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	703
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	704
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	705 <xml name="input_image_file_format">
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 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 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	707 <option value="png" selected="true">png</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	708 <option value="pdf">pdf</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	709 <option value="svg">svg</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	710 <option value="eps">eps</option>
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	711 <option value="plotly">plotly</option>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	712 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	713 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	714
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	715 <xml name="output_dpi">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	716 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	717 label="Image dpi" help=""/>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	718 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	719
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	720 <xml name="output_image_file_format">
15 67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	721 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	722 <change_format>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	723 <when input="output.outFileFormat" value="pdf" format="pdf" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	724 <when input="output.outFileFormat" value="svg" format="svg" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	725 <when input="output.outFileFormat" value="eps" format="eps" />
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	726 <when input="output.outFileFormat" value="plotly" format="html" />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	727 </change_format>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	728 </data>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	729 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	730
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	731 <xml name="output_image_file_format_not_nested">
15 67f3aaf8d49f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 14 diff changeset	732 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	733 <change_format>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	734 <when input="outFileFormat" value="pdf" format="pdf" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	735 <when input="outFileFormat" value="svg" format="svg" />
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	736 <when input="outFileFormat" value="eps" format="eps" />
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	737 <when input="outFileFormat" value="plotly" format="html" />
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	738 </change_format>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	739 </data>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	740 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	741
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	742 <xml name="output_save_matrix_values">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	743 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	744 <filter>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	745 ((
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	746 output['showOutputSettings'] == 'yes' and
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	747 output['saveMatrix'] is True
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	748 ))
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	749 </filter>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	750 </data>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	751 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	752
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	753 <xml name="output_graphic_outputs">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	754 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	755 <filter>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	756 ((
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	757 output['showOutputSettings'] == 'yes' and
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	758 output['saveSortedRegions'] is True
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	759 ))
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	760 </filter>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	761 </data>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	762 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	763
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	764 <xml name="colorMap">
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	765 <param name="colorMap" type="select" label="Color map to use for the heatmap"
12 4039432f51fc planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 11 diff changeset	766 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	767 <option value="RdYlBu" selected="true">RdYlBu</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	768 <option value="Accent">Accent</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	769 <option value="Spectral">Spectral</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	770 <option value="Set1">Set1</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	771 <option value="Set2">Set2</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	772 <option value="Set3">Set3</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	773 <option value="Dark2">Dark2</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	774 <option value="Reds">Reds</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	775 <option value="Oranges">Oranges</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	776 <option value="Greens">Greens</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	777 <option value="Blues">Blues</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	778 <option value="Greys">Greys</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	779 <option value="Purples">Purples</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	780 <option value="Paired">Paired</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	781 <option value="Pastel1">Pastel1</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	782 <option value="Pastel2">Pastel2</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	783 <option value="spring">spring</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	784 <option value="summer">summer</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	785 <option value="autumn">autumn</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	786 <option value="winter">winter</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	787 <option value="hot">hot</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	788 <option value="coolwarm">coolwarm</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	789 <option value="cool">cool</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	790 <option value="seismic">seismic</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	791 <option value="terrain">terrain</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	792 <option value="ocean">ocean</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	793 <option value="rainbow">rainbow</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	794 <option value="bone">bone</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	795 <option value="flag">flag</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	796 <option value="prism">prism</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	797 <option value="cubehelix">cubehelix</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	798 <option value="binary">binary</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	799 <option value="pink">pink</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	800 <option value="gray">gray</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	801 <option value="copper">copper</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	802 <option value="BrBG">BrBG</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	803 <option value="BuGn">BuGn</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	804 <option value="BuPu">BuPu</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	805 <option value="GnBu">GnBu</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	806 <option value="OrRd">OrRd</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	807 <option value="PiYG">PiYG</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	808 <option value="PRGn">PRGn</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	809 <option value="PuOr">PuOr</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	810 <option value="PuRd">PuRd</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	811 <option value="PuBu">PuBu</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	812 <option value="RdBu">RdBu</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	813 <option value="RdGy">RdGy</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	814 <option value="RdPu">RdPu</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	815 <option value="YlGn">YlGn</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	816 <option value="PuBuGn">PuBuGn</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	817 <option value="RdYlGn">RdYlGn</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	818 <option value="YlGnBu">YlGnBu</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	819 <option value="YlOrBr">YlOrBr</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	820 <option value="YlOrRd">YlOrRd</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	821 <option value="gist_gray">gist_gray</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	822 <option value="gist_stern">gist_stern</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	823 <option value="gist_earth">gist_earth</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	824 <option value="gist_yarg">gist_yarg</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	825 <option value="gist_ncar">gist_ncar</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	826 <option value="gist_rainbow">gist_rainbow</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	827 <option value="gist_heat">gist_heat</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	828 <option value="gnuplot">gnuplot</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	829 <option value="gnuplot2">gnuplot2</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	830 <option value="CMRmap">CMRmap</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	831 <option value="bwr">bwr</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	832 <option value="hsv">hsv</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	833 <option value="brg">brg</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	834 <option value="jet">jet</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	835 <option value="afmhot">afmhot</option>
19 057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	836 <option value="Wistia">Wistia</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	837 <option value="cividis">cividis</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	838 <option value="icefire">icefire</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	839 <option value="inferno">inferno</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	840 <option value="magma">magma</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	841 <option value="mako">mako</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	842 <option value="nipy_spectral">nipy_spectral</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	843 <option value="plasma">plasma</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	844 <option value="rocket">rocket</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	845 <option value="tab10">tab10</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	846 <option value="tab20">tab20</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	847 <option value="tab20b">tab20b</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	848 <option value="tab20c">tab20c</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	849 <option value="twilight">twilight</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	850 <option value="twilight_shifted">twilight_shifted</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	851 <option value="viridis">viridis</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	852 <option value="vlag">vlag</option>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	853 <option value="Accent_r">Accent reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	854 <option value="Spectral_r">Spectral reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	855 <option value="Set1_r">Set1 reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	856 <option value="Set2_r">Set2 reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	857 <option value="Set3_r">Set3 reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	858 <option value="Dark2_r">Dark2 reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	859 <option value="Reds_r">Reds reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	860 <option value="Oranges_r">Oranges reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	861 <option value="Greens_r">Greens reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	862 <option value="Blues_r">Blues reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	863 <option value="Greys_r">Greys reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	864 <option value="Purples_r">Purples reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	865 <option value="Paired_r">Paired reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	866 <option value="Pastel1_r">Pastel1 reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	867 <option value="Pastel2_r">Pastel2 reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	868 <option value="spring_r">spring reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	869 <option value="summer_r">summer reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	870 <option value="autumn_r">autumn reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	871 <option value="winter_r">winter reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	872 <option value="hot_r">hot reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	873 <option value="coolwarm_r">coolwarm reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	874 <option value="cool_r">cool reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	875 <option value="seismic_r">seismic reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	876 <option value="terrain_r">terrain reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	877 <option value="ocean_r">ocean reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	878 <option value="rainbow_r">rainbow reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	879 <option value="bone_r">bone reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	880 <option value="flag_r">flag reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	881 <option value="prism_r">prism reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	882 <option value="cubehelix_r">cubehelix reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	883 <option value="binary_r">binary reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	884 <option value="pink_r">pink reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	885 <option value="gray_r">gray reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	886 <option value="copper_r">copper reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	887 <option value="BrBG_r">BrBG reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	888 <option value="BuGn_r">BuGn reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	889 <option value="BuPu_r">BuPu reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	890 <option value="GnBu_r">GnBu reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	891 <option value="OrRd_r">OrRd reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	892 <option value="PiYG_r">PiYG reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	893 <option value="PRGn_r">PRGn reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	894 <option value="PuOr_r">PuOr reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	895 <option value="PuRd_r">PuRd reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	896 <option value="PuBu_r">PuBu reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	897 <option value="RdBu_r">RdBu reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	898 <option value="RdGy_r">RdGy reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	899 <option value="RdPu_r">RdPu reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	900 <option value="YlGn_r">YlGn reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	901 <option value="PuBuGn_r">PuBuGn reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	902 <option value="RdYlBu_r">RdYlBu reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	903 <option value="RdYlGn_r">RdYlGn reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	904 <option value="YlGnBu_r">YlGnBu reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	905 <option value="YlOrBr_r">YlOrBr reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	906 <option value="YlOrRd_r">YlOrRd reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	907 <option value="gist_gray_r">gist_gray reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	908 <option value="gist_stern_r">gist_stern reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	909 <option value="gist_earth_r">gist_earth reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	910 <option value="gist_yarg_r">gist_yarg reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	911 <option value="gist_ncar_r">gist_ncar reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	912 <option value="gist_rainbow_r">gist_rainbow reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	913 <option value="gist_heat_r">gist_heat reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	914 <option value="gnuplot_r">gnuplot reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	915 <option value="gnuplot2_r">gnuplot2 reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	916 <option value="CMRmap_r">CMRmap reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	917 <option value="bwr_r">bwr reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	918 <option value="hsv_r">hsv reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	919 <option value="brg_r">brg reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	920 <option value="jet_r">jet reversed</option>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	921 <option value="afmhot_r">afmhot reversed</option>
19 057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	922 <option value="Wistia_r">Wistia reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	923 <option value="cividis_r">cividis reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	924 <option value="icefire_r">icefire reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	925 <option value="inferno_r">inferno reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	926 <option value="magma_r">magma reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	927 <option value="mako_r">mako reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	928 <option value="nipy_spectral_r">nipy_spectral reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	929 <option value="plasma_r">plasma reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	930 <option value="rocket_r">rocket reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	931 <option value="tab10_r">tab10 reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	932 <option value="tab20_r">tab20 reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	933 <option value="tab20b_r">tab20b reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	934 <option value="tab20c_r">tab20c reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	935 <option value="twilight_r">twilight reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	936 <option value="twilight_shifted_r">twilight_shifted reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	937 <option value="viridis_r">viridis reversed</option>
057ead9b9577 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 18 diff changeset	938 <option value="vlag_r">vlag reversed</option>
0 c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	939 </param>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	940
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	941 </xml>
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	942
c53dcf458fc0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: diff changeset	943 </macros>

Mercurial > repos > bgruening > deeptools_plot_enrichment

annotate deepTools_macros.xml @ 21:d95486ad55e8 draft default tip