deeptools_plot_coverage: deepTools

annotate deepTools_macros.xml @ 18:0f9ad7d1876c draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit beb75870e99ed8ceca69753bf7de546877b3e2ff

author	bgruening
date	Fri, 12 Aug 2016 05:14:58 -0400
parents	4e9fb57c5e7d
children	c7c137f09c0f

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
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	3 <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	4 <conditional name="advancedOpt">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	5 <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	6 <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	7 <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	8 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	9 <when value="no" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	10 <when value="yes">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	11 <yield/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	12 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	13 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	14 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	15
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	16 <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	17 #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	18 --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	19 #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	20 --extendReads
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	21 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	23 $advancedOpt.centerReads
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	26 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	29 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	32 #end if
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	33 #if $advancedOpt.minFragmentLength:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	34 --minFragmentLength $advancedOpt.minFragmentLength
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	35 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	36 #if $advancedOpt.maxFragmentLength:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	37 --maxFragmentLength $advancedOpt.maxFragmentLength
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	38 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	39 </token>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	40
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	41 <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	42 $advancedOpt.metagene
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	43 #if $advancedOpt.transcriptID:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	44 --transcriptID $advancedOpt.transcriptID
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	45 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	46 #if $advancedOpt.exonID:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	47 --exonID $advancedOpt.exonID
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	48 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	49 #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	50 --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	51 #end if
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	52 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	53
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	54 <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	55 <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	56 <expand macro="colorMap" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	57 <expand macro="plotTitle" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	58 <expand macro="plotNumbers" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	59 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	60
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	61 <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	62 #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	63 --zMin $plotting_type.zMin
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	64 #end if
3 89dc332a851a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 2 diff changeset	65 #if str($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	66 --zMax $plotting_type.zMax
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	67 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	68 --colorMap '$plotting_type.colorMap'
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	69 $plotting_type.plotNumbers
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	70 --plotTitle '$plotting_type.plotTitle'
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	71 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	72
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	73
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	74 <xml name="includeZeros">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	75 <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	76 label="Include zeros"
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	77 help="If set, then regions with zero counts for all BAM 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	78 </xml>
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="zMin_zMax">
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	81 <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	82 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	83 <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	84 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	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 <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	88 <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	89 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	90 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	91 <sanitizer>
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	92 <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	93 <add value="\|"/>
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	94 </valid>
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	95 </sanitizer>
582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	96 </param>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	97 </xml>
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 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
18 0f9ad7d1876c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit beb75870e99ed8ceca69753bf7de546877b3e2ff bgruening parents: 17 diff changeset	100 <token name="@WRAPPER_VERSION@">2.3.3</token>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	101 <xml name="requirements">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	102 <requirements>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	103 <requirement type="package" version="2.7.10">python</requirement>
18 0f9ad7d1876c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit beb75870e99ed8ceca69753bf7de546877b3e2ff bgruening parents: 17 diff changeset	104 <requirement type="package" version="2.3.3">deepTools</requirement>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	105 <yield />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	106 </requirements>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	107 <expand macro="stdio" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	108 <version_command>@BINARY@ --version</version_command>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	109 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	110
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	111 <xml name="smoothLength">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	112 <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	113 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	114 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	115 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	116
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	117
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	118 <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	119 <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	120 <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	121 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	122 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	123 <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	124 <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	125 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	126 <when value="no">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	127 <conditional name="clustering">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	128 <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	129 <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	130 <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	131 <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	132 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	133 <when value="kmeans">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	134 <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	135 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	136 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	137 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	138 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	139 </when>
9 4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	140 <when value="hclust">
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	141 <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	142 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	143 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	144 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	145 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	146 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	147 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	148 </when>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	149 <when value="none" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	150 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	151 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	152 <when value="yes" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	153 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	154 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	155
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	156 <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	157 #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	158 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	159 #if int($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	160 --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	161 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	162 #end if
9 4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	163 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	164 #if int($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	165 --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	166 #end if
4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	167 #end if
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	168 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	169 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	170
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	171 <xml name="samFlags">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	172 <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	173 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	174 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	175 <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	176 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	177 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	178 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	179
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	180 <xml name="fragLength">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	181 <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	182 label="Minimum fragment length for inclusion."
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	183 help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	184 <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	185 label="Maximum fragment length for inclusion."
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	186 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	187 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	188
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	189 <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	190 <expand macro="extendReads" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	191 <expand macro="ignoreDuplicates" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	192 <expand macro="centerReads" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	193 <expand macro="minMappingQuality" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	194 <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	195 <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	196 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	197
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	198 <xml name="gtf_options">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	199 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	200 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	201 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	202 <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	203 label="trascript designator"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	204 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	205 <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	206 label="exon designator"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	207 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	208 <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	209 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	210 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	211 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	212 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	213 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	214 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	215
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	216
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	217 <xml name="plotNumbers">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	218 <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	219 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	220 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	221 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	222
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	223 <xml name="extendReads">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	224 <conditional name="doExtendCustom">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	225 <param name="doExtend" type="select" 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	226 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	227 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	228 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	229 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	230 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	231 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	232 <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	233 <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	234 <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	235 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	236 <when value="no" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	237 <when value="yes" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	238 <when value="custom">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	239 <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	240 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	241 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	242 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	243 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	244 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	245
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	246 <xml name="corMethod">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	247 <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	248 <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	249 <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	250 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	251 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	252
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	253 <xml name="distanceBetweenBins">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	254 <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	255 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	256 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	257 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	258 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	259 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	260 considered."/>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	261 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	262
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	263 <xml name="centerReads">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	264 <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	265 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	266 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	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="ignoreDuplicates">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	270 <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	271 label="Ignore duplicates"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	272 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	273 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	274
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	275 <xml name="sortUsing">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	276 <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	277 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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	285 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	286
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	287 <xml name="sortRegions">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	288 <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	289 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	290 <option value="no">no ordering</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	291 <option value="descend" selected="true">descending order</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	292 <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	293 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	294 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	295
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	296 <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	297 <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	298 label="Minimum mapping quality"
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	299 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	300 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	301
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	302 <xml name="skipZeros">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	303 <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	304 label ="Skip zeros"
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	305 help ="If set, then zero counts that happen for all BAM 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	306 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	307
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	308 <xml name="fragmentLength">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	309 <param argument="--fragmentLength" 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	310 label="Fragment length used for the sequencing"
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	311 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	312 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	313
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	314 <xml name="scaleFactor">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	315 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	316 help="When used in combination with --normalizeTo1x or
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	317 --normalizeUsingRPKM, the computed scaling factor will
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	318 be multiplied by the given scale factor." />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	319 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	320
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	321 <xml name="scaleFactors">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	322 <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	323 <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	324 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	325
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	326 <xml name="stdio">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	327 <stdio>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	328 <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	329 <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	330 <regex match="Error:" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	331 <regex match="Exception:" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	332 <regex match="EXception:" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	333 <regex match="Traceback" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	334 </stdio>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	335 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	336
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	337 <xml name="pseudocount">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	338 <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	339 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	340
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	341 <token name="@REFERENCES@">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	342
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	343 .. class:: infomark
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 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	346
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	347 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	348
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	349 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	350
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	351 .. _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	352 .. _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	353 .. _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	354
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	355 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	356 <xml name="citations">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	357 <citations>
15 582a05c586ba planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 14 diff changeset	358 <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	359 <yield />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	360 </citations>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	361 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	362
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	363 <xml name="multiple_input_bams">
10 d135576cd41c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 9 diff changeset	364 <param argument="--bamfiles" type="data" format="bam" min="1"
d135576cd41c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 9 diff changeset	365 label="Bam file" multiple="true"
12 752d2d85e6af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c bgruening parents: 10 diff changeset	366 help=""/>
10 d135576cd41c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 9 diff changeset	367 </xml>
d135576cd41c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 9 diff changeset	368
d135576cd41c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 9 diff changeset	369 <xml name="multiple_input_bams_min2">
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	370 <param argument="--bamfiles" type="data" format="bam" min="2"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	371 label="Bam file" multiple="true"
12 752d2d85e6af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c bgruening parents: 10 diff changeset	372 help=""/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	373 </xml>
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 <xml 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	376 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	377 label="Bigwig file"
4 1a6309cecf71 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 3 diff changeset	378 help="A Bigwig file."/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	379 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	380
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	381 <xml name="plotTitle">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	382 <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	383 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	384 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	385 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	386
9 4679da05d86c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 8 diff changeset	387
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	388 <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	389 <![CDATA[
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	390 #set files=[]
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	391 #set labels=[]
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	392 #for $counter, $bamfile in enumerate($bamfiles):
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	393 ln -s "${bamfile}" "./${counter}.bam" &&
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	394 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	395 #silent $files.append('%s.bam' % $counter)
14 8fefd05b0e3f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356 bgruening parents: 12 diff changeset	396 #silent $labels.append("'%s'" % ($bamfile.display_name))
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	397 #end for
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	398 ]]>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	399 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	400
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	401 <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	402 <![CDATA[
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	403 #set files=[]
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	404 #set labels=[]
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	405 #for $counter, $bigwig in enumerate($bigwigfiles):
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	406 ln -s "${bigwig}" "${counter}.bw" &&
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	407 #silent $files.append('%s.bw' % $counter)
14 8fefd05b0e3f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356 bgruening parents: 12 diff changeset	408 #silent $labels.append("'%s'" % ($bigwig.display_name))
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	409 #end for
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	410 ]]>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	411 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	412
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	413 <xml name="blacklist">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	414 <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	415 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	416 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	417 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	418
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	419 <token name="@blacklist@">
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	420 <![CDATA[
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	421 #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	422 #set blfiles=[]
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	423 #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	424 #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	425 #end for
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	426 #if $blfiles != ["'None'"]:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	427 --blackListFileName #echo ' '.join($blfiles)#
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	428 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	429 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	430 ]]>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	431 </token>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	432
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	433 <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	434 <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	435 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	436 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	437 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	438
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	439 <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	440 <![CDATA[
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	441 #set files=[]
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	442 #set labels=[]
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	443 #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	444 #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	445 #silent $labels.append("'%s'" % $f.display_name)
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	446 #end for
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	447 #if len($files) > 0:
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	448 --BED #echo ' '.join($files)#
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	449 --regionLabels #echo ' '.join($labels)#
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	450 #end if
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	451 ]]>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	452 </token>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	453
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	454 <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	455 <conditional name="source">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	456 <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	457 <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	458 <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	459 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	460 <when value="cached">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	461 <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	462 <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	463 <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	464 <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	465 </options>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	466 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	467 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	468 <when value="history">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	469 <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	470 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	471 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	472 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	473
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	474 <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	475 #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	476 --genome $source.input1
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	477 #else:
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	478 --genome "$source.input1_2bit.fields.path"
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	479 #end if
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	480 </token>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	481
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	482 <xml name="effectiveGenomeSize">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	483 <conditional name="effectiveGenomeSize">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	484 <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	485 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	486 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	487 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	488 <option value="93260000">ce10 (93260000)</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	489 <option value="121400000">dm3 (121400000)</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	490 <option value="2451960000" selected="true">hg19 (2451960000)</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	491 <option value="2150570000">mm9 (2150570000)</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	492 <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	493 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	494 <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	495 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	496 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	497 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	498 <when value="2150570000" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	499 <when value="2451960000" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	500 <when value="121400000" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	501 <when value="93260000" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	502 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	503 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	504
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	505 <xml name="skipNAs">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	506 <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	507 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	508 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	509 (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	510 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	511 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	512 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	513 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	514 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	515 (default: False)" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	516 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	517
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	518 <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	519 <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	520 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	521
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	522 <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	523 <conditional name="output" >
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	524 <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	525 <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	526 <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	527 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	528 <when value="no" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	529 <when value="yes">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	530 <yield />
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	531 <param name="saveSortedRegions" type="boolean"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	532 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	533 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	534 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	535 </when>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	536 </conditional>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	537 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	538
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	539
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	540 <xml name="input_image_file_format">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	541 <param argument="--outFileFormat" type="select" label="Image file format">
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	542 <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	543 <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	544 <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	545 <option value="eps">eps</option>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	546 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	547 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	548
17 4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	549 <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	550 <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	551 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	552 </xml>
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	553
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	554 <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	555 <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	556 <change_format>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	557 <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	558 <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	559 <when input="output.outFileFormat" value="eps" format="eps" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	560 </change_format>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	561 </data>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	562 </xml>
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="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	565 <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	566 <change_format>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	567 <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	568 <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	569 <when input="outFileFormat" value="eps" format="eps" />
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	570 </change_format>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	571 </data>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	572 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	573
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	574 <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	575 <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	576 <filter>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	577 ((
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	578 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	579 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	580 ))
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	581 </filter>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	582 </data>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	583 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	584
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	585 <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	586 <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	587 <filter>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	588 ((
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	589 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	590 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	591 ))
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	592 </filter>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	593 </data>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	594 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	595
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	596 <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	597 <param name="colorMap" type="select" label="Color map to use for the heatmap"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	598 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
4e9fb57c5e7d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 16 diff changeset	599 multiple="true">
0 fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	600 <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	601 <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	602 <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	603 <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	604 <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	605 <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	606 <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	607 <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	608 <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	609 <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	610 <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	611 <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	612 <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	613 <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	614 <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	615 <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	616 <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	617 <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	618 <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	619 <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	620 <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	621 <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	622 <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	623 <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	624 <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	625 <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	626 <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	627 <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	628 <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	629 <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	630 <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	631 <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	632 <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	633 <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	634 <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	635 <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	636 <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	637 <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	638 <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	639 <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	640 <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	641 <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	642 <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	643 <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	644 <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	645 <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	646 <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	647 <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	648 <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	649 <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	650 <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	651 <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	652 <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	653 <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	654 <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	655 <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	656 <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	657 <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	658 <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	659 <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	660 <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	661 <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	662 <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	663 <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	664 <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	665 <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	666 <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	667 <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	668 <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	669 <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	670 <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	671 <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	672 <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	673 <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	674 <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	675 <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	676 <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	677 <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	678 <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	679 <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	680 <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	681 <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	682 <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	683 <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	684 <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	685 <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	686 <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	687 <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	688 <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	689 <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	690 <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	691 <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	692 <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	693 <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	694 <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	695 <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	696 <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	697 <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	698 <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	699 <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	700 <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	701 <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	702 <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	703 <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	704 <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	705 <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	706 <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	707 <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	708 <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	709 <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	710 <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	711 <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	712 <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	713 <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	714 <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	715 <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	716 <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	717 <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	718 <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	719 <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	720 <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	721 <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	722 <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	723 <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	724 <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	725 <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	726 <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	727 <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	728 <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	729 <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	730 <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	731 <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	732 <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	733 <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	734 <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	735 <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	736 <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	737 <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	738 </param>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	739
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	740 </xml>
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	741
fd4a79e7e5f0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: diff changeset	742 </macros>

Mercurial > repos > bgruening > deeptools_plot_coverage

annotate deepTools_macros.xml @ 18:0f9ad7d1876c draft