deeptools_bam_coverage: deepTools

annotate deepTools_macros.xml @ 42:0d2ba04b8261 draft default tip

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

author	bgruening
date	Thu, 01 Jun 2023 10:23:48 +0000
parents	a4ecef241a6d
children

rev	line source
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	1 <macros>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	2
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
42 0d2ba04b8261 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 41 diff changeset	4 <token name="@TOOL_VERSION@">3.5.2</token>
0d2ba04b8261 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 41 diff changeset	5 <token name="@GALAXY_VERSION@">20.01</token>
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	6 <xml name="requirements">
f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	7 <requirements>
42 0d2ba04b8261 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 41 diff changeset	8 <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	9 <requirement type="package" version="1.9">samtools</requirement>
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	10 </requirements>
f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	11 <expand macro="stdio" />
f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	12 <version_command>@BINARY@ --version</version_command>
f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	13 </xml>
f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	14
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	15 <xml name="advancedOpt_scaffold">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	16 <conditional name="advancedOpt">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	17 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	18 <option value="no" selected="true">no</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	19 <option value="yes">yes</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	20 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	21 <when value="no" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	22 <when value="yes">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	23 <yield/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	24 </when>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	25 </conditional>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	26 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	27
29 573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	28 <token name="@PLOTWIDTHHEIGHT@">
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	29 --plotWidth '$advancedOpt.plotWidth'
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	30 --plotHeight '$advancedOpt.plotHeight'
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	31 </token>
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	32
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	33 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	34 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	35 label="Plot height"
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	36 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	37
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	38 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	39 label="Plot width"
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	40 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	41 </xml>
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	42
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	43 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	44 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	45 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	46 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	47 --extendReads
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	48 #end if
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	49 $advancedOpt.ignoreDuplicates
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	50 $advancedOpt.centerReads
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	51 #if $advancedOpt.minMappingQuality:
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	52 --minMappingQuality '$advancedOpt.minMappingQuality'
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	53 #end if
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	54 #if $advancedOpt.samFlagInclude:
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	55 --samFlagInclude $advancedOpt.samFlagInclude
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	56 #end if
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	57 #if $advancedOpt.samFlagExclude:
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	58 --samFlagExclude $advancedOpt.samFlagExclude
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	59 #end if
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	60 #if $advancedOpt.minFragmentLength:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	61 --minFragmentLength $advancedOpt.minFragmentLength
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	62 #end if
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	63 #if $advancedOpt.maxFragmentLength:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	64 --maxFragmentLength $advancedOpt.maxFragmentLength
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	65 #end if
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	66 </token>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	67
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	68 <token name="@ADVANCED_OPTS_GTF@">
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	69 $advancedOpt.metagene
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	70 #if $advancedOpt.transcriptID:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	71 --transcriptID $advancedOpt.transcriptID
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	72 #end if
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	73 #if $advancedOpt.exonID:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	74 --exonID $advancedOpt.exonID
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	75 #end if
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	76 #if $advancedOpt.transcript_id_designator:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	77 --transcript_id_designator $advancedOpt.transcript_id_designator
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	78 #end if
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	79 </token>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	80
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	81 <xml name="heatmap_options">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	82 <expand macro="zMin_zMax" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	83 <expand macro="colorMap" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	84 <expand macro="plotTitle" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	85 <expand macro="plotNumbers" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	86 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	87
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	88 <token name="@HEATMAP_OPTIONS@">
7 a259f484f884 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	89 #if str($plotting_type.zMin) != "":
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	90 --zMin $plotting_type.zMin
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	91 #end if
7 a259f484f884 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	92 #if str($plotting_type.zMax) != "":
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	93 --zMax $plotting_type.zMax
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	94 #end if
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	95 --colorMap '$plotting_type.colorMap'
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	96 $plotting_type.plotNumbers
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	97 --plotTitle '$plotting_type.plotTitle'
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	98 </token>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	99
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	100
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	101 <xml name="includeZeros">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	102 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	103 label="Include zeros"
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	104 help="If set, then regions with zero counts for all BAM/CRAM files are included. The default behavior is to ignore such regions." />
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	105 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	106
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	107 <xml name="zMin_zMax">
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	108 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	109 help="If not specified the value is set automatically."/>
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	110 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	111 help="If not specified the value is set automatically."/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	112 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	113
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	114 <xml name="region_limit_operation">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	115 <param argument="--region" type="text" value=""
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	116 label="Region of the genome to limit the operation to"
19 205f1536914d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	117 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".">
205f1536914d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	118 <sanitizer>
205f1536914d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	119 <valid initial="string.letters,string.digits">
205f1536914d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	120 <add value="\|"/>
23 3e96983c0057 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 22 diff changeset	121 <add value=":"/>
35 7e55c0415e71 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 34 diff changeset	122 <add value="."/>
19 205f1536914d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	123 </valid>
205f1536914d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	124 </sanitizer>
205f1536914d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	125 </param>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	126 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	127
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	128 <xml name="smoothLength">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	129 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
8 9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	130 label="Smooth values using the following length (in bases)"
9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	131 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	132 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	133
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	134
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	135 <xml name="kmeans_clustering">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	136 <conditional name="used_multiple_regions">
2 fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	137 <param name="used_multiple_regions_options" type="select"
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	138 label="Did you compute the matrix with more than one groups of regions?"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	139 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	140 <option value="yes">Yes, I used multiple groups of regions</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	141 <option value="no">No, I used only one group</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	142 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	143 <when value="no">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	144 <conditional name="clustering">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	145 <param name="clustering_options" type="select" label="Clustering algorithm">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	146 <option value="none">No clustering</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	147 <option value="kmeans">Kmeans clustering</option>
13 892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	148 <option value="hclust">Hierarchical clustering</option>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	149 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	150 <when value="kmeans">
2 fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	151 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
8 9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	152 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	153 This only works for data that is not grouped, otherwise only the first group will be clustered.
7 a259f484f884 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	154 If more specific clustering methods are required it is advisable to save the underlying matrix and
8 9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	155 run the clustering using other software."/>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	156 </when>
13 892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	157 <when value="hclust">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	158 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	159 help="WARNING: This option causes the tool to run for a very long time! When this option is
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	160 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	161 This only works for data that is not grouped, otherwise only the first group will be clustered.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	162 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	163 If more specific clustering methods are required it is advisable to save the underlying matrix and
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	164 run the clustering using other software."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	165 </when>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	166 <when value="none" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	167 </conditional>
40 211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	168 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	169 label="Compute the silhouette score for each region"
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	170 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	171 The silhouette score is a measure of how similar a region is to other regions in the same cluster as
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	172 opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	173 The silhouette evaluation can be very slow when you have more than 100 000 regions." />
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	174 </when>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	175 <when value="yes" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	176 </conditional>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	177 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	178
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	179 <token name="@KMEANS_CLUSTERING@">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	180 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	181 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	182 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	183 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	184 #end if
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	185 #end if
13 892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	186 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	187 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	188 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	189 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	190 #end if
40 211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	191 $advancedOpt.used_multiple_regions.silhouette
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	192 #end if
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	193 </token>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	194
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	195 <xml name="samFlags">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	196 <param argument="--samFlagInclude" type="integer" optional="True" value=""
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	197 label="Include reads based on the SAM flag"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	198 help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	199 <param argument="--samFlagExclude" type="integer" optional="True" value=""
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	200 label="Exclude reads based on the SAM flag"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	201 help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	202 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	203
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	204 <xml name="fragLength">
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	205 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	206 label="Minimum fragment length for inclusion."
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	207 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	208 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	209 label="Maximum fragment length for inclusion."
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	210 help="A value of 0 (the default) is equivalent to no maximum." />
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	211 </xml>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	212
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	213 <xml name="read_processing_options">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	214 <expand macro="extendReads" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	215 <expand macro="ignoreDuplicates" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	216 <expand macro="centerReads" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	217 <expand macro="minMappingQuality" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	218 <expand macro="samFlags" />
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	219 <expand macro="fragLength" />
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	220 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	221
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	222 <xml name="gtf_options">
32 33d88fda6240 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c bgruening parents: 30 diff changeset	223 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	224 label="Use a metagene model"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	225 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	226 <param argument="--transcriptID" optional="True" value="transcript" type="text"
36 e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	227 label="transcript designator"
40 211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	228 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	229 <param argument="--exonID" optional="True" value="exon" type="text"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	230 label="exon designator"
40 211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	231 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	232 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	233 label="transcriptID key designator"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	234 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	235 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	236 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	237 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	238 </xml>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	239
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	240
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	241 <xml name="plotNumbers">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	242 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
2 fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	243 label="Plot the correlation value"
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	244 help="If set, then the correlation number is plotted on top of the heatmap."/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	245 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	246
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	247 <xml name="extendReads">
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	248 <conditional name="doExtendCustom">
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	249 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	250 help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
8 9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	251 By default each read mate is extended.
9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	252 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	253 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	254 Reads are only extended if --extendReads is set to a value greater than the read length. NOTE: For spliced-read data, this option is not
9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	255 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	256 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	257 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	258 <option value="custom">A custom length, which will be applied to ALL reads.</option>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	259 </param>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	260 <when value="no" />
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	261 <when value="yes" />
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	262 <when value="custom">
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	263 <param name="extendReadsValue" type="integer" value="300" min="1"
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	264 label="Extend reads to the given average fragment size"
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	265 help="Extend all reads to this length" />
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	266 </when>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	267 </conditional>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	268 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	269
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	270 <xml name="corMethod">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	271 <param argument="--corMethod" type="select" label="Correlation method">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	272 <option value="spearman" selected="True">Spearman</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	273 <option value="pearson">Pearson</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	274 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	275 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	276
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	277 <xml name="distanceBetweenBins">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	278 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	279 label="Distance between bins"
11 bbfcc5bbb3db planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: 9 diff changeset	280 help="By default, multiBamSummary considers consecutive bins of
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	281 the specified 'Bin size'. However, to reduce the
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	282 computation time, a larger distance between bins can
8 9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	283 be given. Larger distances result in fewer bins being
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	284 considered."/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	285 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	286
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	287 <xml name="centerReads">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	288 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	289 label="Center regions with respect to the fragment length"
8 9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	290 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	291 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	292
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	293 <xml name="ignoreDuplicates">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	294 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	295 label="Ignore duplicates"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	296 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	297 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	298
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	299 <xml name="sortUsing">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	300 <param argument="--sortUsing" type="select" label="Method used for sorting"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	301 help="For each row the method is computed.">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	302 <option value="mean" selected="true">mean</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	303 <option value="median">median</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	304 <option value="min">min</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	305 <option value="max">max</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	306 <option value="sum">sum</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	307 <option value="region_length">region length</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	308 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	309 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	310
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	311 <xml name="sortRegionsComputeMatrix">
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	312 <param argument="--sortRegions" type="select" label="Sort regions"
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	313 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	314 <option value="no">no ordering</option>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	315 <option value="keep" selected="true">maintain the same ordering as the input files</option>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	316 <option value="descend">descending order</option>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	317 <option value="ascend">ascending order</option>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	318 </param>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	319 </xml>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	320
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	321 <xml name="sortRegions">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	322 <param argument="--sortRegions" type="select" label="Sort regions"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	323 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	324 <option value="no">maintain the same ordering as the input files</option>
26 651432fd3139 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 25 diff changeset	325 <option value="descend" selected="true">descending order</option>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	326 <option value="ascend">ascending order</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	327 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	328 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	329
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	330 <xml name="minMappingQuality">
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	331 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	332 label="Minimum mapping quality"
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	333 help= "If set, only reads with a mapping quality score at least this high are considered."/>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	334 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	335
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	336 <xml name="skipZeros">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	337 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	338 label ="Skip zeros"
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	339 help ="If set, then zero counts that happen for all BAM/CRAM files given are ignored. This may result in fewer considered regions." />
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	340 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	341
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	342 <xml name="fragmentLength">
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	343 <param argument="--fragmentLength" type="integer" min="1" optional="true"
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	344 label="Fragment length used for the sequencing"
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	345 help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	346 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	347
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	348 <xml name="scaleFactor">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	349 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	350 help="The computed scaling factor will be multiplied by this (default 1)." />
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	351 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	352
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	353 <xml name="scaleFactors">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	354 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	355 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	356 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	357
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	358 <xml name="stdio">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	359 <stdio>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	360 <exit_code range="1:" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	361 <exit_code range=":-1" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	362 <regex match="Error:" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	363 <regex match="Exception:" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	364 <regex match="EXception:" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	365 <regex match="Traceback" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	366 </stdio>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	367 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	368
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	369 <xml name="pseudocount">
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	370 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	371 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	372 <token name="@REFERENCES@">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	373
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	374 .. class:: infomark
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	375
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	376 For more information on the tools, please visit our `help site`_.
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	377
40 211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	378 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	379
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	380 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	381
40 211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	382 .. _Biostars: http://biostars.org
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	383 .. _on github: http://github.com
2 fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	384 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	385 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2 fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	386 .. _help site: https://deeptools.readthedocs.org/
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	387
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	388 </token>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	389 <xml name="citations">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	390 <citations>
19 205f1536914d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	391 <citation type="doi">10.1093/nar/gkw257</citation>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	392 <yield />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	393 </citations>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	394 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	395
29 573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	396 <xml name="multiple_input_bams" tokens="MIN">
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	397 <conditional name="multibam_conditional">
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	398 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	399 <option value="No" selected="true">No</option>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	400 <option value="Yes">Yes</option>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	401 </param>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	402 <when value="No">
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	403 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	404 label="BAM/CRAM file" multiple="true"
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	405 help=""/>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	406 </when>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	407 <when value="Yes">
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	408 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	409 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	410 </repeat>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	411 </when>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	412 </conditional>
14 390f015a4438 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 13 diff changeset	413 </xml>
390f015a4438 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 13 diff changeset	414
29 573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	415 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	416 <conditional name="multibigwig_conditional">
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	417 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	418 is vital to you, select Yes below.">
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	419 <option value="No" selected="true">No</option>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	420 <option value="Yes">Yes</option>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	421 </param>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	422 <when value="No">
29 573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	423 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	424 label="@LABEL@"
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	425 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	426 </when>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	427 <when value="Yes">
29 573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	428 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	429 <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	430 </repeat>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	431 </when>
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	432 </conditional>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	433 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	434
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	435 <xml name="custom_sample_labels">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	436 <conditional name="custom_sample_labels_conditional">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	437 <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	438 <option value="No" selected="true">No, use sample names in the history</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	439 <option value="Yes">Yes, I want to specify new labels</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	440 </param>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	441 <when value="No">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	442 </when>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	443 <when value="Yes">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	444 <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., "sample 1" "sample 2")">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	445 <sanitizer>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	446 <valid initial="string.printable">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	447 </valid>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	448 </sanitizer>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	449 </param>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	450 </when>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	451 </conditional>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	452 </xml>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	453
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	454 <xml name="plotTitle">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	455 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	456 label="Title of the plot"
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	457 help="Title of the plot, to be printed on top of the generated image." />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	458 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	459
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	460 <xml name="legendLocation">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	461 <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	462 <option value="best" selected="true">Best (automatic)</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	463 <option value="upper-right">upper-right</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	464 <option value="upper-left">upper-left</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	465 <option value="upper-center">upper-center</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	466 <option value="lower-right">lower-right</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	467 <option value="lower-left">lower-left</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	468 <option value="lower-center">lower-center</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	469 <option value="center-right">center-right</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	470 <option value="center-left">center-left</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	471 <option value="center">center</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	472 <option value="none">none (only works for heatmaps</option>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	473 </param>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	474 </xml>
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	475
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	476 <xml name="labelRotation">
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	477 <param argument="--labelRotation" type="integer" value="0"
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	478 label="Rotation of the X-axis labels (in degrees)"
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	479 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	480 </xml>
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	481
13 892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	482
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	483 <token name="@multiple_input_bams@">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	484 <![CDATA[
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
42 0d2ba04b8261 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 41 diff changeset	486 #set custom_labels=$custom_sample_labels_conditional.labels
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	487 #end if
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	488 #set files=[]
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	489 #set labels=[]
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	490 #import re
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	491 #if $multibam_conditional.orderMatters == "No":
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	492 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	493 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
35 7e55c0415e71 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 34 diff changeset	494 ln -s '${bamfile}' './${counter}.bam' &&
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	495 #if $bamfile.ext == 'bam':
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	497 #else:
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	499 #end if
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	500 #silent $files.append("'%s.bam'" % $counter)
42 0d2ba04b8261 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 41 diff changeset	501 #silent $labels.append("'%s'" % $identifier)
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	502 #end for
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	503 #else:
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	504 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
35 7e55c0415e71 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 34 diff changeset	506 ln -s '${f.bamfiles}' './${counter}.bam' &&
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	507 #if $f.bamfiles.ext == 'bam':
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	508 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	509 #else:
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	510 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	511 #end if
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	512 #silent $files.append("'%s.bam'" % $counter)
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	513 #silent $labels.append("'%s'" % $identifier)
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	514 #end for
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	515 #end if
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	516 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	517 #set labels=custom_labels
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	518 #end if
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	519 ]]>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	520 </token>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	521
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	522 <token name="@multiple_input_bigwigs@">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	523 <![CDATA[
38 fc5d69ca44e8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 37 diff changeset	524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
42 0d2ba04b8261 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 41 diff changeset	525 #set custom_labels=$custom_sample_labels_conditional.labels
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	526 #end if
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	527 #set files=[]
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	528 #set labels=[]
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	529 #import re
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	530 #if $multibigwig_conditional.orderMatters == "No":
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	531 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
29 573924c7f94f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 27 diff changeset	532 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
35 7e55c0415e71 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 34 diff changeset	533 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	534 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	535 #silent $labels.append("'%s'" % $identifier)
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	536 #end for
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	537 #else:
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	538 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	539 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
35 7e55c0415e71 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 34 diff changeset	540 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	541 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
27 f82a4c20e3bf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 26 diff changeset	542 #silent $labels.append("'%s'" % $identifier)
25 bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	543 #end for
bc24fb3f9e91 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 24 diff changeset	544 #end if
38 fc5d69ca44e8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 37 diff changeset	545 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
37 f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	546 #set labels=custom_labels
f854d3209894 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 36 diff changeset	547 #end if
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	548 ]]>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	549 </token>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	550
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	551 <xml name="blacklist">
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	552 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	553 label="Blacklisted regions in BED/GTF format"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	554 help="One or more files containing regions to exclude from the analysis" />
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	555 </xml>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	556
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	557 <token name="@blacklist@">
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	558 <![CDATA[
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	559 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	560 #set blfiles=[]
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	561 #for $f in $advancedOpt.blackListFileName:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	562 #silent $blfiles.append("'%s'" % $f)
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	563 #end for
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	564 #if $blfiles != ["'None'"]:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	565 --blackListFileName #echo ' '.join($blfiles)#
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	566 #end if
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	567 #end if
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	568 ]]>
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	569 </token>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	570
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	571 <xml name="multiple_bed">
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	572 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	573 label="Regions in BED/GTF format"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	574 help="One or more files containing regions to include in the analysis" />
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	575 </xml>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	576
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	577 <token name="@multiple_bed@">
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	578 <![CDATA[
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	579 #set files=[]
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	580 #set labels=[]
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	581 #for $f in $BED:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	582 #silent $files.append("'%s'" % $f)
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	583 #silent $labels.append("'%s'" % $f.display_name)
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	584 #end for
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	585 #if len($files) > 0:
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	586 --BED #echo ' '.join($files)#
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	587 --regionLabels #echo ' '.join($labels)#
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	588 #end if
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	589 ]]>
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	590 </token>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	591
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	592 <xml name="reference_genome_source">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	593 <conditional name="source">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	594 <param name="ref_source" type="select" label="Reference genome">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	595 <option value="cached">locally cached</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	596 <option value="history">in your history</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	597 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	598 <when value="cached">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	599 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	600 <options from_data_table="lastz_seqs">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	601 <filter type="sort_by" column="1" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	602 <validator type="no_options" message="No indexes are available." />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	603 </options>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	604 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	605 </when>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	606 <when value="history">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	607 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	608 </when>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	609 </conditional>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	610 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	611
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	612 <token name="@reference_genome_source@">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	613 #if $source.ref_source=="history":
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	614 --genome $source.input1
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	615 #else:
35 7e55c0415e71 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 34 diff changeset	616 --genome '$source.input1_2bit.fields.path'
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	617 #end if
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	618 </token>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	619
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	620 <xml name="effectiveGenomeSize">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	621 <conditional name="effectiveGenomeSize">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	622 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
2 fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	623 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	624 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	625 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	626 <option value="93260000">ce10 (93260000)</option>
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	627 <option value="130428560">dm3 (130428560)</option>
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	628 <option value="125464728">dm6 (125464728)</option>
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	629 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	630 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	631 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	632 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	633 <option value="specific">user specified</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	634 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	635 <when value="specific">
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	636 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	637 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	638 </when>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	639 <when value="93260000" />
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	640 <when value="130428560" />
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	641 <when value="125464728" />
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	642 <when value="2685511504" />
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	643 <when value="2701495761" />
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	644 <when value="2304947926" />
6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	645 <when value="2308125349" />
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	646 </conditional>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	647 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	648
1 66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	649 <xml name="skipNAs">
66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	650 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	651 label="Ignore missing data?"
66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	652 help="This parameter determines if non-covered regions
66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	653 (regions without overlapping reads) in a bam/bigWig file
66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	654 should be skipped. The default is to treat those
66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	655 regions as having a value of zero. The decision to
66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	656 skip non-covered regions depends on the interpretation
8 9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	657 of the data. Non-covered regions may represent, for
9e8925f84444 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	658 example, repetitive regions that should be ignored.
1 66947f20a9a8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	659 (default: False)" />
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	660 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	661
39 77b364ae7821 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 38 diff changeset	662 <xml name="skipZeroOverZero">
77b364ae7821 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 38 diff changeset	663 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
77b364ae7821 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 38 diff changeset	664 help="Skip bins where BOTH files lack coverage.">
77b364ae7821 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 38 diff changeset	665 <option value="" selected="true">No</option>
77b364ae7821 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 38 diff changeset	666 <option value="--skipZeroOverZero">Yes, skip them.</option>
77b364ae7821 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 38 diff changeset	667 </param>
77b364ae7821 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 38 diff changeset	668 </xml>
77b364ae7821 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 38 diff changeset	669
36 e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	670 <xml name="exactScaling">
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	671 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	672 label="Compute an exact scaling factor"
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	673 help="Compute an exact scaling factor rather than one based on
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	674 sampled reads. This is only useful in cases where you are
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	675 filtering some alignments out AND this are both rare and
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	676 tend to clump together in the genome. In such cases the
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	677 region-based sampling employed by deepTools would produce
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	678 inaccurate scaling factors. Note that this option results
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	679 in the process taking significantly more time to complete." />
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	680 </xml>
e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	681
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	682 <xml name="input_save_matrix_values">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	683 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	684 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	685
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	686 <xml name="input_graphic_output_settings">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	687 <conditional name="output" >
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	688 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	689 <option value="no" selected="true">no</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	690 <option value="yes">yes</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	691 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	692 <when value="no" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	693 <when value="yes">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	694 <yield />
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	695 <param name="saveSortedRegions" type="boolean"
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	696 argument="--outFileSortedRegions"
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	697 label="Save the regions after skipping zeros or min/max threshold values"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	698 help="The order of the regions in the file follows the sorting order selected. This is useful,
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	699 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	700 </when>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	701 </conditional>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	702 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	703
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	704
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	705 <xml name="input_image_file_format">
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	706 <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	707 <option value="png" selected="true">png</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	708 <option value="pdf">pdf</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	709 <option value="svg">svg</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	710 <option value="eps">eps</option>
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	711 <option value="plotly">plotly</option>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	712 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	713 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	714
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	715 <xml name="output_dpi">
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	716 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	717 label="Image dpi" help=""/>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	718 </xml>
96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	719
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	720 <xml name="output_image_file_format">
36 e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	721 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	722 <change_format>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	723 <when input="output.outFileFormat" value="pdf" format="pdf" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	724 <when input="output.outFileFormat" value="svg" format="svg" />
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	725 <when input="output.outFileFormat" value="eps" format="eps" />
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	726 <when input="output.outFileFormat" value="plotly" format="html" />
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	727 </change_format>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	728 </data>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	729 </xml>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	730
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	731 <xml name="output_image_file_format_not_nested">
36 e57332b94d4f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 35 diff changeset	732 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
3 be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	733 <change_format>
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	734 <when input="outFileFormat" value="pdf" format="pdf" />
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	735 <when input="outFileFormat" value="svg" format="svg" />
be8d749ea54b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	736 <when input="outFileFormat" value="eps" format="eps" />
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	737 <when input="outFileFormat" value="plotly" format="html" />
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	738 </change_format>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	739 </data>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	740 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	741
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	742 <xml name="output_save_matrix_values">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	743 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	744 <filter>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	745 ((
2 fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	746 output['showOutputSettings'] == 'yes' and
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	747 output['saveMatrix'] is True
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	748 ))
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	749 </filter>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	750 </data>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	751 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	752
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	753 <xml name="output_graphic_outputs">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	754 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	755 <filter>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	756 ((
2 fee7b464d8e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	757 output['showOutputSettings'] == 'yes' and
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	758 output['saveSortedRegions'] is True
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	759 ))
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	760 </filter>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	761 </data>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	762 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	763
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	764 <xml name="colorMap">
21 96057da0d8d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	765 <param name="colorMap" type="select" label="Color map to use for the heatmap"
33 6a5dfb2c0c60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 32 diff changeset	766 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	767 <option value="RdYlBu" selected="true">RdYlBu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	768 <option value="Accent">Accent</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	769 <option value="Spectral">Spectral</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	770 <option value="Set1">Set1</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	771 <option value="Set2">Set2</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	772 <option value="Set3">Set3</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	773 <option value="Dark2">Dark2</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	774 <option value="Reds">Reds</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	775 <option value="Oranges">Oranges</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	776 <option value="Greens">Greens</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	777 <option value="Blues">Blues</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	778 <option value="Greys">Greys</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	779 <option value="Purples">Purples</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	780 <option value="Paired">Paired</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	781 <option value="Pastel1">Pastel1</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	782 <option value="Pastel2">Pastel2</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	783 <option value="spring">spring</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	784 <option value="summer">summer</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	785 <option value="autumn">autumn</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	786 <option value="winter">winter</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	787 <option value="hot">hot</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	788 <option value="coolwarm">coolwarm</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	789 <option value="cool">cool</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	790 <option value="seismic">seismic</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	791 <option value="terrain">terrain</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	792 <option value="ocean">ocean</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	793 <option value="rainbow">rainbow</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	794 <option value="bone">bone</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	795 <option value="flag">flag</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	796 <option value="prism">prism</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	797 <option value="cubehelix">cubehelix</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	798 <option value="binary">binary</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	799 <option value="pink">pink</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	800 <option value="gray">gray</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	801 <option value="copper">copper</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	802 <option value="BrBG">BrBG</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	803 <option value="BuGn">BuGn</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	804 <option value="BuPu">BuPu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	805 <option value="GnBu">GnBu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	806 <option value="OrRd">OrRd</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	807 <option value="PiYG">PiYG</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	808 <option value="PRGn">PRGn</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	809 <option value="PuOr">PuOr</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	810 <option value="PuRd">PuRd</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	811 <option value="PuBu">PuBu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	812 <option value="RdBu">RdBu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	813 <option value="RdGy">RdGy</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	814 <option value="RdPu">RdPu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	815 <option value="YlGn">YlGn</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	816 <option value="PuBuGn">PuBuGn</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	817 <option value="RdYlGn">RdYlGn</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	818 <option value="YlGnBu">YlGnBu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	819 <option value="YlOrBr">YlOrBr</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	820 <option value="YlOrRd">YlOrRd</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	821 <option value="gist_gray">gist_gray</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	822 <option value="gist_stern">gist_stern</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	823 <option value="gist_earth">gist_earth</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	824 <option value="gist_yarg">gist_yarg</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	825 <option value="gist_ncar">gist_ncar</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	826 <option value="gist_rainbow">gist_rainbow</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	827 <option value="gist_heat">gist_heat</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	828 <option value="gnuplot">gnuplot</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	829 <option value="gnuplot2">gnuplot2</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	830 <option value="CMRmap">CMRmap</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	831 <option value="bwr">bwr</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	832 <option value="hsv">hsv</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	833 <option value="brg">brg</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	834 <option value="jet">jet</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	835 <option value="afmhot">afmhot</option>
40 211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	836 <option value="Wistia">Wistia</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	837 <option value="cividis">cividis</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	838 <option value="icefire">icefire</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	839 <option value="inferno">inferno</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	840 <option value="magma">magma</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	841 <option value="mako">mako</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	842 <option value="nipy_spectral">nipy_spectral</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	843 <option value="plasma">plasma</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	844 <option value="rocket">rocket</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	845 <option value="tab10">tab10</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	846 <option value="tab20">tab20</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	847 <option value="tab20b">tab20b</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	848 <option value="tab20c">tab20c</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	849 <option value="twilight">twilight</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	850 <option value="twilight_shifted">twilight_shifted</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	851 <option value="viridis">viridis</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	852 <option value="vlag">vlag</option>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	853 <option value="Accent_r">Accent reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	854 <option value="Spectral_r">Spectral reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	855 <option value="Set1_r">Set1 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	856 <option value="Set2_r">Set2 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	857 <option value="Set3_r">Set3 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	858 <option value="Dark2_r">Dark2 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	859 <option value="Reds_r">Reds reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	860 <option value="Oranges_r">Oranges reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	861 <option value="Greens_r">Greens reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	862 <option value="Blues_r">Blues reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	863 <option value="Greys_r">Greys reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	864 <option value="Purples_r">Purples reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	865 <option value="Paired_r">Paired reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	866 <option value="Pastel1_r">Pastel1 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	867 <option value="Pastel2_r">Pastel2 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	868 <option value="spring_r">spring reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	869 <option value="summer_r">summer reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	870 <option value="autumn_r">autumn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	871 <option value="winter_r">winter reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	872 <option value="hot_r">hot reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	873 <option value="coolwarm_r">coolwarm reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	874 <option value="cool_r">cool reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	875 <option value="seismic_r">seismic reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	876 <option value="terrain_r">terrain reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	877 <option value="ocean_r">ocean reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	878 <option value="rainbow_r">rainbow reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	879 <option value="bone_r">bone reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	880 <option value="flag_r">flag reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	881 <option value="prism_r">prism reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	882 <option value="cubehelix_r">cubehelix reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	883 <option value="binary_r">binary reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	884 <option value="pink_r">pink reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	885 <option value="gray_r">gray reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	886 <option value="copper_r">copper reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	887 <option value="BrBG_r">BrBG reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	888 <option value="BuGn_r">BuGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	889 <option value="BuPu_r">BuPu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	890 <option value="GnBu_r">GnBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	891 <option value="OrRd_r">OrRd reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	892 <option value="PiYG_r">PiYG reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	893 <option value="PRGn_r">PRGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	894 <option value="PuOr_r">PuOr reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	895 <option value="PuRd_r">PuRd reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	896 <option value="PuBu_r">PuBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	897 <option value="RdBu_r">RdBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	898 <option value="RdGy_r">RdGy reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	899 <option value="RdPu_r">RdPu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	900 <option value="YlGn_r">YlGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	901 <option value="PuBuGn_r">PuBuGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	902 <option value="RdYlBu_r">RdYlBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	903 <option value="RdYlGn_r">RdYlGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	904 <option value="YlGnBu_r">YlGnBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	905 <option value="YlOrBr_r">YlOrBr reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	906 <option value="YlOrRd_r">YlOrRd reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	907 <option value="gist_gray_r">gist_gray reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	908 <option value="gist_stern_r">gist_stern reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	909 <option value="gist_earth_r">gist_earth reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	910 <option value="gist_yarg_r">gist_yarg reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	911 <option value="gist_ncar_r">gist_ncar reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	912 <option value="gist_rainbow_r">gist_rainbow reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	913 <option value="gist_heat_r">gist_heat reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	914 <option value="gnuplot_r">gnuplot reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	915 <option value="gnuplot2_r">gnuplot2 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	916 <option value="CMRmap_r">CMRmap reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	917 <option value="bwr_r">bwr reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	918 <option value="hsv_r">hsv reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	919 <option value="brg_r">brg reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	920 <option value="jet_r">jet reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	921 <option value="afmhot_r">afmhot reversed</option>
40 211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	922 <option value="Wistia_r">Wistia reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	923 <option value="cividis_r">cividis reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	924 <option value="icefire_r">icefire reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	925 <option value="inferno_r">inferno reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	926 <option value="magma_r">magma reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	927 <option value="mako_r">mako reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	928 <option value="nipy_spectral_r">nipy_spectral reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	929 <option value="plasma_r">plasma reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	930 <option value="rocket_r">rocket reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	931 <option value="tab10_r">tab10 reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	932 <option value="tab20_r">tab20 reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	933 <option value="tab20b_r">tab20b reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	934 <option value="tab20c_r">tab20c reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	935 <option value="twilight_r">twilight reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	936 <option value="twilight_shifted_r">twilight_shifted reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	937 <option value="viridis_r">viridis reversed</option>
211d14085e1f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 39 diff changeset	938 <option value="vlag_r">vlag reversed</option>
0 af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	939 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	940
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	941 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	942
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	943 </macros>

Mercurial > repos > bgruening > deeptools_bam_coverage

annotate deepTools_macros.xml @ 42:0d2ba04b8261 draft default tip