deeptools_plot_coverage: deepTools

annotate deepTools_macros.xml @ 31:1d9d0ef3ab37 draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754

author	bgruening
date	Thu, 05 Apr 2018 10:41:19 -0400
parents	ce44b1c88849
children	003a83043303

rev	line source
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	1 <macros>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	2
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
31 1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 30 diff changeset	4 <token name="@WRAPPER_VERSION@">3.0.2</token>
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	5 <xml name="requirements">
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	6 <requirements>
31 1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 30 diff changeset	7 <requirement type="package" version="3.0.2">deeptools</requirement>
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	8 <requirement type="package" version="1.7">samtools</requirement>
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	9 </requirements>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	10 <expand macro="stdio" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	11 <version_command>@BINARY@ --version</version_command>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	12 </xml>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	13
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	14 <xml name="advancedOpt_scaffold">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	15 <conditional name="advancedOpt">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	16 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	17 <option value="no" selected="true">no</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	18 <option value="yes">yes</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	19 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	20 <when value="no" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	21 <when value="yes">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	22 <yield/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	23 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	24 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	25 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	26
25 bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	27 <token name="@PLOTWIDTHHEIGHT@">
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	28 --plotWidth '$advancedOpt.plotWidth'
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	29 --plotHeight '$advancedOpt.plotHeight'
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	30 </token>
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	31
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	32 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	33 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	34 label="Plot height"
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	36
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	37 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	38 label="Plot width"
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	39 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	40 </xml>
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	41
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	42 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	43 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	44 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	45 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	46 --extendReads
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	47 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	48 $advancedOpt.ignoreDuplicates
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	49 $advancedOpt.centerReads
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	50 #if $advancedOpt.minMappingQuality:
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	51 --minMappingQuality '$advancedOpt.minMappingQuality'
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	52 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	53 #if $advancedOpt.samFlagInclude:
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	54 --samFlagInclude $advancedOpt.samFlagInclude
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	55 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	56 #if $advancedOpt.samFlagExclude:
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	57 --samFlagExclude $advancedOpt.samFlagExclude
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	58 #end if
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	59 #if $advancedOpt.minFragmentLength:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	60 --minFragmentLength $advancedOpt.minFragmentLength
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	61 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	62 #if $advancedOpt.maxFragmentLength:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	63 --maxFragmentLength $advancedOpt.maxFragmentLength
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	64 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	65 </token>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	66
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	67 <token name="@ADVANCED_OPTS_GTF@">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	68 $advancedOpt.metagene
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	69 #if $advancedOpt.transcriptID:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	70 --transcriptID $advancedOpt.transcriptID
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	71 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	72 #if $advancedOpt.exonID:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	73 --exonID $advancedOpt.exonID
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	74 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	75 #if $advancedOpt.transcript_id_designator:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	76 --transcript_id_designator $advancedOpt.transcript_id_designator
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	77 #end if
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	78 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	79
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	80 <xml name="heatmap_options">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	81 <expand macro="zMin_zMax" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	82 <expand macro="colorMap" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	83 <expand macro="plotTitle" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	84 <expand macro="plotNumbers" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	85 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	86
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	87 <token name="@HEATMAP_OPTIONS@">
3 89dc332a851a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 2 diff changeset	88 #if str($plotting_type.zMin) != "":
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	89 --zMin $plotting_type.zMin
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	90 #end if
3 89dc332a851a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 2 diff changeset	91 #if str($plotting_type.zMax) != "":
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	92 --zMax $plotting_type.zMax
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	93 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	94 --colorMap '$plotting_type.colorMap'
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	95 $plotting_type.plotNumbers
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	96 --plotTitle '$plotting_type.plotTitle'
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	97 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	98
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	99
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	100 <xml name="includeZeros">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	101 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	102 label="Include zeros"
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	103 help="If set, then regions with zero counts for all BAM/CRAM files are included. The default behavior is to ignore such regions." />
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	104 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	105
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	106 <xml name="zMin_zMax">
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	107 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	108 help="If not specified the value is set automatically."/>
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	109 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	110 help="If not specified the value is set automatically."/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	111 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	112
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	113 <xml name="region_limit_operation">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	114 <param argument="--region" type="text" value=""
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	115 label="Region of the genome to limit the operation to"
15 582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	116 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".">
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	117 <sanitizer>
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	118 <valid initial="string.letters,string.digits">
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	119 <add value="\|"/>
19 c7c137f09c0f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 18 diff changeset	120 <add value=":"/>
31 1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 30 diff changeset	121 <add value="."/>
15 582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	122 </valid>
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	123 </sanitizer>
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	124 </param>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	125 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	126
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	127 <xml name="smoothLength">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	128 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	129 label="Smooth values using the following length (in bases)"
1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	130 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	131 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	132
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	133
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	134 <xml name="kmeans_clustering">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	135 <conditional name="used_multiple_regions">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	136 <param name="used_multiple_regions_options" type="select"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	137 label="Did you compute the matrix with more than one groups of regions?"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	138 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	139 <option value="yes">Yes, I used multiple groups of regions</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	140 <option value="no">No, I used only one group</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	141 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	142 <when value="no">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	143 <conditional name="clustering">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	144 <param name="clustering_options" type="select" label="Clustering algorithm">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	145 <option value="none">No clustering</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	146 <option value="kmeans">Kmeans clustering</option>
9 4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	147 <option value="hclust">Hierarchical clustering</option>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	148 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	149 <when value="kmeans">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	150 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	151 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	152 This only works for data that is not grouped, otherwise only the first group will be clustered.
3 89dc332a851a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 2 diff changeset	153 If more specific clustering methods are required it is advisable to save the underlying matrix and
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	154 run the clustering using other software."/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	155 </when>
9 4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	156 <when value="hclust">
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	157 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	158 help="WARNING: This option causes the tool to run for a very long time! When this option is
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	159 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	160 This only works for data that is not grouped, otherwise only the first group will be clustered.
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	161 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	162 If more specific clustering methods are required it is advisable to save the underlying matrix and
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	163 run the clustering using other software."/>
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	164 </when>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	165 <when value="none" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	166 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	167 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	168 <when value="yes" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	169 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	170 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	171
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	172 <token name="@KMEANS_CLUSTERING@">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	173 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	174 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	175 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	176 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	177 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	178 #end if
9 4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	179 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	180 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	181 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	182 #end if
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	183 #end if
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	184 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	185 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	186
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	187 <xml name="samFlags">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	188 <param argument="--samFlagInclude" type="integer" optional="True" value=""
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	189 label="Include reads based on the SAM flag"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	190 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."/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	191 <param argument="--samFlagExclude" type="integer" optional="True" value=""
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	192 label="Exclude reads based on the SAM flag"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	193 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."/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	194 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	195
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	196 <xml name="fragLength">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	197 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	198 label="Minimum fragment length for inclusion."
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	199 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	200 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	201 label="Maximum fragment length for inclusion."
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	202 help="A value of 0 (the default) is equivalent to no maximum." />
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	203 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	204
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	205 <xml name="read_processing_options">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	206 <expand macro="extendReads" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	207 <expand macro="ignoreDuplicates" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	208 <expand macro="centerReads" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	209 <expand macro="minMappingQuality" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	210 <expand macro="samFlags" />
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	211 <expand macro="fragLength" />
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	212 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	213
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	214 <xml name="gtf_options">
28 29e5735f9499 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c bgruening parents: 26 diff changeset	215 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	216 label="Use a metagene model"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	217 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." />
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	218 <param argument="--transcriptID" optional="True" value="transcript" type="text"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	219 label="trascript designator"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	220 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	221 <param argument="--exonID" optional="True" value="exon" type="text"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	222 label="exon designator"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	223 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	224 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	225 label="transcriptID key designator"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	226 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	227 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	228 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	229 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	230 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	231
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	232
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	233 <xml name="plotNumbers">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	234 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	235 label="Plot the correlation value"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	236 help="If set, then the correlation number is plotted on top of the heatmap."/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	237 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	238
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	239 <xml name="extendReads">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	240 <conditional name="doExtendCustom">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	241 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	242 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.
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	243 By default each read mate is extended.
1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	244 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	245 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	246 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
1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	247 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	248 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	249 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	250 <option value="custom">A custom length, which will be applied to ALL reads.</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	251 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	252 <when value="no" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	253 <when value="yes" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	254 <when value="custom">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	255 <param name="extendReadsValue" type="integer" value="300" min="1"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	256 label="Extend reads to the given average fragment size"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	257 help="Extend all reads to this length" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	258 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	259 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	260 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	261
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	262 <xml name="corMethod">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	263 <param argument="--corMethod" type="select" label="Correlation method">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	264 <option value="spearman" selected="True">Spearman</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	265 <option value="pearson">Pearson</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	266 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	267 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	268
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	269 <xml name="distanceBetweenBins">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	270 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	271 label="Distance between bins"
7 cc1de49667a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: 5 diff changeset	272 help="By default, multiBamSummary considers consecutive bins of
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	273 the specified 'Bin size'. However, to reduce the
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	274 computation time, a larger distance between bins can
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	275 be given. Larger distances result in fewer bins being
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	276 considered."/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	277 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	278
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	279 <xml name="centerReads">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	280 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	281 label="Center regions with respect to the fragment length"
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	282 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."/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	283 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	284
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	285 <xml name="ignoreDuplicates">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	286 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	287 label="Ignore duplicates"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	288 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." />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	289 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	290
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	291 <xml name="sortUsing">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	292 <param argument="--sortUsing" type="select" label="Method used for sorting"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	293 help="For each row the method is computed.">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	294 <option value="mean" selected="true">mean</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	295 <option value="median">median</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	296 <option value="min">min</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	297 <option value="max">max</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	298 <option value="sum">sum</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	299 <option value="region_length">region length</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	300 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	301 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	302
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	303 <xml name="sortRegionsComputeMatrix">
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	304 <param argument="--sortRegions" type="select" label="Sort regions"
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	305 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	306 <option value="no">no ordering</option>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	307 <option value="keep" selected="true">maintain the same ordering as the input files</option>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	308 <option value="descend">descending order</option>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	309 <option value="ascend">ascending order</option>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	310 </param>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	311 </xml>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	312
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	313 <xml name="sortRegions">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	314 <param argument="--sortRegions" type="select" label="Sort regions"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	315 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	316 <option value="no">maintain the same ordering as the input files</option>
22 ce408ea2ef08 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 21 diff changeset	317 <option value="descend" selected="true">descending order</option>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	318 <option value="ascend">ascending order</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	319 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	320 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	321
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	322 <xml name="minMappingQuality">
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	323 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	324 label="Minimum mapping quality"
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	325 help= "If set, only reads with a mapping quality score at least this high are considered."/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	326 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	327
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	328 <xml name="skipZeros">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	329 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	330 label ="Skip zeros"
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	331 help ="If set, then zero counts that happen for all BAM/CRAM files given are ignored. This may result in fewer considered regions." />
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	332 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	333
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	334 <xml name="fragmentLength">
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	335 <param argument="--fragmentLength" type="integer" min="1" optional="true"
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	336 label="Fragment length used for the sequencing"
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	337 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 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	338 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	339
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	340 <xml name="scaleFactor">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	341 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	342 help="The computed scaling factor will be multiplied by this (default 1)." />
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	343 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	344
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	345 <xml name="scaleFactors">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	346 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	347 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	348 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	349
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	350 <xml name="stdio">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	351 <stdio>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	352 <exit_code range="1:" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	353 <exit_code range=":-1" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	354 <regex match="Error:" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	355 <regex match="Exception:" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	356 <regex match="EXception:" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	357 <regex match="Traceback" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	358 </stdio>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	359 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	360
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	361 <xml name="pseudocount">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	362 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	363 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	364
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	365 <token name="@REFERENCES@">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	366
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	367 .. class:: infomark
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	368
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	369 For more information on the tools, please visit our `help site`_.
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	370
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	371 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	372
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	373 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	374
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	375 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	376 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	377 .. _help site: https://deeptools.readthedocs.org/
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	378
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	379 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	380 <xml name="citations">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	381 <citations>
15 582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	382 <citation type="doi">10.1093/nar/gkw257</citation>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	383 <yield />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	384 </citations>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	385 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	386
25 bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	387 <xml name="multiple_input_bams" tokens="MIN">
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	388 <conditional name="multibam_conditional">
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	389 <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.">
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	390 <option value="No" selected="true">No</option>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	391 <option value="Yes">Yes</option>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	392 </param>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	393 <when value="No">
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	394 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	395 label="BAM/CRAM file" multiple="true"
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	396 help=""/>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	397 </when>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	398 <when value="Yes">
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	399 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	400 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	401 </repeat>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	402 </when>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	403 </conditional>
10 d135576cd41c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 9 diff changeset	404 </xml>
d135576cd41c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 9 diff changeset	405
25 bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	406 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	407 <conditional name="multibigwig_conditional">
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	408 <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
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	409 is vital to you, select Yes below.">
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	410 <option value="No" selected="true">No</option>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	411 <option value="Yes">Yes</option>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	412 </param>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	413 <when value="No">
25 bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	414 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	415 label="@LABEL@"
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	416 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	417 </when>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	418 <when value="Yes">
25 bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	419 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	420 <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."/>
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	421 </repeat>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	422 </when>
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	423 </conditional>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	424 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	425
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	426 <xml name="plotTitle">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	427 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	428 label="Title of the plot"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	429 help="Title of the plot, to be printed on top of the generated image." />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	430 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	431
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	432 <xml name="labelRotation">
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	433 <param argument="--labelRotation" type="integer" value="0"
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	434 label="Rotation of the X-axis labels (in degrees)"
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	435 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." />
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	436 </xml>
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	437
9 4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	438
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	439 <token name="@multiple_input_bams@">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	440 <![CDATA[
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	441 #set files=[]
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	442 #set labels=[]
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	443 #import re
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	444 #if $multibam_conditional.orderMatters == "No":
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	445 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	446 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
31 1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 30 diff changeset	447 ln -s '${bamfile}' './${counter}.bam' &&
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	448 #if $bamfile.ext == 'bam':
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	449 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	450 #else:
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	451 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	452 #end if
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	453 #silent $files.append("'%s.bam'" % $counter)
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	454 #silent $labels.append("'%s'" % identifier)
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	455 #end for
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	456 #else:
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	457 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	458 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
31 1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 30 diff changeset	459 ln -s '${f.bamfiles}' './${counter}.bam' &&
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	460 #if $f.bamfiles.ext == 'bam':
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	461 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	462 #else:
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	463 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	464 #end if
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	465 #silent $files.append("'%s.bam'" % $counter)
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	466 #silent $labels.append("'%s'" % $identifier)
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	467 #end for
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	468 #end if
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	469 ]]>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	470 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	471
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	472 <token name="@multiple_input_bigwigs@">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	473 <![CDATA[
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	474 #set files=[]
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	475 #set labels=[]
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	476 #import re
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	477 #if $multibigwig_conditional.orderMatters == "No":
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	478 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
25 bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 23 diff changeset	479 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
31 1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 30 diff changeset	480 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	481 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	482 #silent $labels.append("'%s'" % $identifier)
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	483 #end for
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	484 #else:
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	485 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	486 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
31 1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 30 diff changeset	487 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	488 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
23 5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 22 diff changeset	489 #silent $labels.append("'%s'" % $identifier)
21 34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	490 #end for
34721558d320 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 20 diff changeset	491 #end if
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	492 ]]>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	493 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	494
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	495 <xml name="blacklist">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	496 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	497 label="Blacklisted regions in BED/GTF format"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	498 help="One or more files containing regions to exclude from the analysis" />
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	499 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	500
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	501 <token name="@blacklist@">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	502 <![CDATA[
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	503 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	504 #set blfiles=[]
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	505 #for $f in $advancedOpt.blackListFileName:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	506 #silent $blfiles.append("'%s'" % $f)
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	507 #end for
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	508 #if $blfiles != ["'None'"]:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	509 --blackListFileName #echo ' '.join($blfiles)#
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	510 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	511 #end if
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	512 ]]>
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	513 </token>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	514
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	515 <xml name="multiple_bed">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	516 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	517 label="Regions in BED/GTF format"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	518 help="One or more files containing regions to include in the analysis" />
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	519 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	520
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	521 <token name="@multiple_bed@">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	522 <![CDATA[
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	523 #set files=[]
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	524 #set labels=[]
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	525 #for $f in $BED:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	526 #silent $files.append("'%s'" % $f)
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	527 #silent $labels.append("'%s'" % $f.display_name)
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	528 #end for
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	529 #if len($files) > 0:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	530 --BED #echo ' '.join($files)#
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	531 --regionLabels #echo ' '.join($labels)#
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	532 #end if
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	533 ]]>
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	534 </token>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	535
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	536 <xml name="reference_genome_source">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	537 <conditional name="source">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	538 <param name="ref_source" type="select" label="Reference genome">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	539 <option value="cached">locally cached</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	540 <option value="history">in your history</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	541 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	542 <when value="cached">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	543 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	544 <options from_data_table="lastz_seqs">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	545 <filter type="sort_by" column="1" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	546 <validator type="no_options" message="No indexes are available." />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	547 </options>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	548 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	549 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	550 <when value="history">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	551 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	552 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	553 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	554 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	555
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	556 <token name="@reference_genome_source@">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	557 #if $source.ref_source=="history":
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	558 --genome $source.input1
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	559 #else:
31 1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 30 diff changeset	560 --genome '$source.input1_2bit.fields.path'
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	561 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	562 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	563
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	564 <xml name="effectiveGenomeSize">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	565 <conditional name="effectiveGenomeSize">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	566 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	567 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.
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	568 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	569 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	570 <option value="93260000">ce10 (93260000)</option>
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	571 <option value="130428560">dm3 (130428560)</option>
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	572 <option value="125464728">dm6 (125464728)</option>
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	573 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	574 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	575 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	576 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	577 <option value="specific">user specified</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	578 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	579 <when value="specific">
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	580 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	581 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	582 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	583 <when value="93260000" />
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	584 <when value="130428560" />
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	585 <when value="125464728" />
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	586 <when value="2685511504" />
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	587 <when value="2701495761" />
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	588 <when value="2304947926" />
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	589 <when value="2308125349" />
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	590 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	591 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	592
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	593 <xml name="skipNAs">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	594 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	595 label="Ignore missing data?"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	596 help="This parameter determines if non-covered regions
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	597 (regions without overlapping reads) in a bam/bigWig file
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	598 should be skipped. The default is to treat those
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	599 regions as having a value of zero. The decision to
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	600 skip non-covered regions depends on the interpretation
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	601 of the data. Non-covered regions may represent, for
1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	602 example, repetitive regions that should be ignored.
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	603 (default: False)" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	604 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	605
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	606 <xml name="input_save_matrix_values">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	607 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	608 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	609
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	610 <xml name="input_graphic_output_settings">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	611 <conditional name="output" >
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	612 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	613 <option value="no" selected="true">no</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	614 <option value="yes">yes</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	615 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	616 <when value="no" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	617 <when value="yes">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	618 <yield />
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	619 <param name="saveSortedRegions" type="boolean"
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	620 argument="--outFileSortedRegions"
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	621 label="Save the regions after skipping zeros or min/max threshold values"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	622 help="The order of the regions in the file follows the sorting order selected. This is useful,
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	623 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	624 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	625 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	626 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	627
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	628
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	629 <xml name="input_image_file_format">
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	630 <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 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	631 <option value="png" selected="true">png</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	632 <option value="pdf">pdf</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	633 <option value="svg">svg</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	634 <option value="eps">eps</option>
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	635 <option value="plotly">plotly</option>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	636 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	637 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	638
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	639 <xml name="output_dpi">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	640 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	641 label="Image dpi" help=""/>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	642 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	643
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	644 <xml name="output_image_file_format">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	645 <data format="png" name="outFileName" label="${tool.name} image">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	646 <change_format>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	647 <when input="output.outFileFormat" value="pdf" format="pdf" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	648 <when input="output.outFileFormat" value="svg" format="svg" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	649 <when input="output.outFileFormat" value="eps" format="eps" />
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	650 <when input="output.outFileFormat" value="plotly" format="html" />
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	651 </change_format>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	652 </data>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	653 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	654
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	655 <xml name="output_image_file_format_not_nested">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	656 <data format="png" name="outFileName" label="${tool.name} image">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	657 <change_format>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	658 <when input="outFileFormat" value="pdf" format="pdf" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	659 <when input="outFileFormat" value="svg" format="svg" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	660 <when input="outFileFormat" value="eps" format="eps" />
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	661 <when input="outFileFormat" value="plotly" format="html" />
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	662 </change_format>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	663 </data>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	664 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	665
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	666 <xml name="output_save_matrix_values">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	667 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	668 <filter>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	669 ((
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	670 output['showOutputSettings'] == 'yes' and
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	671 output['saveMatrix'] is True
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	672 ))
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	673 </filter>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	674 </data>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	675 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	676
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	677 <xml name="output_graphic_outputs">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	678 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	679 <filter>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	680 ((
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	681 output['showOutputSettings'] == 'yes' and
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	682 output['saveSortedRegions'] is True
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	683 ))
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	684 </filter>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	685 </data>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	686 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	687
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	688 <xml name="colorMap">
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	689 <param name="colorMap" type="select" label="Color map to use for the heatmap"
29 79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 28 diff changeset	690 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	691 <option value="RdYlBu" selected="true">RdYlBu</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	692 <option value="Accent">Accent</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	693 <option value="Spectral">Spectral</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	694 <option value="Set1">Set1</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	695 <option value="Set2">Set2</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	696 <option value="Set3">Set3</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	697 <option value="Dark2">Dark2</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	698 <option value="Reds">Reds</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	699 <option value="Oranges">Oranges</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	700 <option value="Greens">Greens</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	701 <option value="Blues">Blues</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	702 <option value="Greys">Greys</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	703 <option value="Purples">Purples</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	704 <option value="Paired">Paired</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	705 <option value="Pastel1">Pastel1</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	706 <option value="Pastel2">Pastel2</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	707 <option value="spring">spring</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	708 <option value="summer">summer</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	709 <option value="autumn">autumn</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	710 <option value="winter">winter</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	711 <option value="hot">hot</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	712 <option value="coolwarm">coolwarm</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	713 <option value="cool">cool</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	714 <option value="seismic">seismic</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	715 <option value="terrain">terrain</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	716 <option value="ocean">ocean</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	717 <option value="rainbow">rainbow</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	718 <option value="bone">bone</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	719 <option value="flag">flag</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	720 <option value="prism">prism</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	721 <option value="cubehelix">cubehelix</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	722 <option value="binary">binary</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	723 <option value="pink">pink</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	724 <option value="gray">gray</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	725 <option value="copper">copper</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	726 <option value="BrBG">BrBG</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	727 <option value="BuGn">BuGn</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	728 <option value="BuPu">BuPu</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	729 <option value="GnBu">GnBu</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	730 <option value="OrRd">OrRd</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	731 <option value="PiYG">PiYG</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	732 <option value="PRGn">PRGn</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	733 <option value="PuOr">PuOr</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	734 <option value="PuRd">PuRd</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	735 <option value="PuBu">PuBu</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	736 <option value="RdBu">RdBu</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	737 <option value="RdGy">RdGy</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	738 <option value="RdPu">RdPu</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	739 <option value="YlGn">YlGn</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	740 <option value="PuBuGn">PuBuGn</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	741 <option value="RdYlGn">RdYlGn</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	742 <option value="YlGnBu">YlGnBu</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	743 <option value="YlOrBr">YlOrBr</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	744 <option value="YlOrRd">YlOrRd</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	745 <option value="gist_gray">gist_gray</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	746 <option value="gist_stern">gist_stern</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	747 <option value="gist_earth">gist_earth</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	748 <option value="gist_yarg">gist_yarg</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	749 <option value="gist_ncar">gist_ncar</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	750 <option value="gist_rainbow">gist_rainbow</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	751 <option value="gist_heat">gist_heat</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	752 <option value="gnuplot">gnuplot</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	753 <option value="gnuplot2">gnuplot2</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	754 <option value="CMRmap">CMRmap</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	755 <option value="bwr">bwr</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	756 <option value="hsv">hsv</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	757 <option value="brg">brg</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	758 <option value="jet">jet</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	759 <option value="afmhot">afmhot</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	760 <option value="Accent_r">Accent reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	761 <option value="Spectral_r">Spectral reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	762 <option value="Set1_r">Set1 reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	763 <option value="Set2_r">Set2 reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	764 <option value="Set3_r">Set3 reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	765 <option value="Dark2_r">Dark2 reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	766 <option value="Reds_r">Reds reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	767 <option value="Oranges_r">Oranges reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	768 <option value="Greens_r">Greens reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	769 <option value="Blues_r">Blues reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	770 <option value="Greys_r">Greys reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	771 <option value="Purples_r">Purples reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	772 <option value="Paired_r">Paired reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	773 <option value="Pastel1_r">Pastel1 reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	774 <option value="Pastel2_r">Pastel2 reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	775 <option value="spring_r">spring reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	776 <option value="summer_r">summer reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	777 <option value="autumn_r">autumn reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	778 <option value="winter_r">winter reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	779 <option value="hot_r">hot reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	780 <option value="coolwarm_r">coolwarm reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	781 <option value="cool_r">cool reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	782 <option value="seismic_r">seismic reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	783 <option value="terrain_r">terrain reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	784 <option value="ocean_r">ocean reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	785 <option value="rainbow_r">rainbow reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	786 <option value="bone_r">bone reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	787 <option value="flag_r">flag reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	788 <option value="prism_r">prism reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	789 <option value="cubehelix_r">cubehelix reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	790 <option value="binary_r">binary reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	791 <option value="pink_r">pink reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	792 <option value="gray_r">gray reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	793 <option value="copper_r">copper reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	794 <option value="BrBG_r">BrBG reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	795 <option value="BuGn_r">BuGn reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	796 <option value="BuPu_r">BuPu reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	797 <option value="GnBu_r">GnBu reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	798 <option value="OrRd_r">OrRd reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	799 <option value="PiYG_r">PiYG reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	800 <option value="PRGn_r">PRGn reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	801 <option value="PuOr_r">PuOr reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	802 <option value="PuRd_r">PuRd reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	803 <option value="PuBu_r">PuBu reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	804 <option value="RdBu_r">RdBu reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	805 <option value="RdGy_r">RdGy reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	806 <option value="RdPu_r">RdPu reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	807 <option value="YlGn_r">YlGn reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	808 <option value="PuBuGn_r">PuBuGn reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	809 <option value="RdYlBu_r">RdYlBu reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	810 <option value="RdYlGn_r">RdYlGn reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	811 <option value="YlGnBu_r">YlGnBu reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	812 <option value="YlOrBr_r">YlOrBr reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	813 <option value="YlOrRd_r">YlOrRd reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	814 <option value="gist_gray_r">gist_gray reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	815 <option value="gist_stern_r">gist_stern reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	816 <option value="gist_earth_r">gist_earth reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	817 <option value="gist_yarg_r">gist_yarg reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	818 <option value="gist_ncar_r">gist_ncar reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	819 <option value="gist_rainbow_r">gist_rainbow reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	820 <option value="gist_heat_r">gist_heat reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	821 <option value="gnuplot_r">gnuplot reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	822 <option value="gnuplot2_r">gnuplot2 reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	823 <option value="CMRmap_r">CMRmap reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	824 <option value="bwr_r">bwr reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	825 <option value="hsv_r">hsv reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	826 <option value="brg_r">brg reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	827 <option value="jet_r">jet reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	828 <option value="afmhot_r">afmhot reversed</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	829 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	830
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	831 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	832
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	833 </macros>

Mercurial > repos > bgruening > deeptools_plot_coverage

annotate deepTools_macros.xml @ 31:1d9d0ef3ab37 draft