deeptools_compute_matrix_operations: deepTools

annotate deepTools_macros.xml @ 20:e6d0bff01239 draft default tip

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412

author	bgruening
date	Wed, 27 Sep 2023 20:30:41 +0000
parents	7ef978dc1b8a
children

rev	line source
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	1 <macros>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	2
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
20 e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	4 <token name="@TOOL_VERSION@">3.5.4</token>
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	5 <token name="@GALAXY_VERSION@">22.05</token>
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	6 <xml name="requirements">
000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	7 <requirements>
19 7ef978dc1b8a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 bgruening parents: 18 diff changeset	8 <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	9 <requirement type="package" version="1.9">samtools</requirement>
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	10 </requirements>
000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	11 <expand macro="stdio" />
000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	12 <version_command>@BINARY@ --version</version_command>
000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	13 </xml>
000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	14
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	15 <xml name="advancedOpt_scaffold">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	16 <conditional name="advancedOpt">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	17 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	18 <option value="no" selected="true">no</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	19 <option value="yes">yes</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	20 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	21 <when value="no" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	22 <when value="yes">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	23 <yield/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	24 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	25 </conditional>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	26 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	27
4 d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	28 <token name="@PLOTWIDTHHEIGHT@">
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	29 --plotWidth '$advancedOpt.plotWidth'
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	30 --plotHeight '$advancedOpt.plotHeight'
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	31 </token>
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	32
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	33 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	34 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	35 label="Plot height"
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	36 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	37
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	38 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	39 label="Plot width"
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	40 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	41 </xml>
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	42
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	43 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	44 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	45 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	46 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	47 --extendReads
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	48 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	49 $advancedOpt.ignoreDuplicates
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	50 $advancedOpt.centerReads
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	51 #if $advancedOpt.minMappingQuality:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	52 --minMappingQuality '$advancedOpt.minMappingQuality'
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	53 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	54 #if $advancedOpt.samFlagInclude:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	55 --samFlagInclude $advancedOpt.samFlagInclude
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	56 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	57 #if $advancedOpt.samFlagExclude:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	58 --samFlagExclude $advancedOpt.samFlagExclude
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	59 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	60 #if $advancedOpt.minFragmentLength:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	61 --minFragmentLength $advancedOpt.minFragmentLength
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	62 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	63 #if $advancedOpt.maxFragmentLength:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	64 --maxFragmentLength $advancedOpt.maxFragmentLength
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	65 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	66 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	67
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	68 <token name="@ADVANCED_OPTS_GTF@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	69 $advancedOpt.metagene
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	70 #if $advancedOpt.transcriptID:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	71 --transcriptID $advancedOpt.transcriptID
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	72 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	73 #if $advancedOpt.exonID:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	74 --exonID $advancedOpt.exonID
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	75 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	76 #if $advancedOpt.transcript_id_designator:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	77 --transcript_id_designator $advancedOpt.transcript_id_designator
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	78 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	79 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	80
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	81 <xml name="heatmap_options">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	82 <expand macro="zMin_zMax" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	83 <expand macro="colorMap" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	84 <expand macro="plotTitle" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	85 <expand macro="plotNumbers" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	86 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	87
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	88 <token name="@HEATMAP_OPTIONS@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	89 #if str($plotting_type.zMin) != "":
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	90 --zMin $plotting_type.zMin
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	91 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	92 #if str($plotting_type.zMax) != "":
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	93 --zMax $plotting_type.zMax
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	94 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	95 --colorMap '$plotting_type.colorMap'
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	96 $plotting_type.plotNumbers
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	97 --plotTitle '$plotting_type.plotTitle'
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	98 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	99
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	100
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	101 <xml name="includeZeros">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	102 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	103 label="Include zeros"
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 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 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	105 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	106
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	107 <xml name="zMin_zMax">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	108 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	109 help="If not specified the value is set automatically."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	110 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	111 help="If not specified the value is set automatically."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	112 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	113
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	114 <xml name="region_limit_operation">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	115 <param argument="--region" type="text" value=""
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	116 label="Region of the genome to limit the operation to"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	117 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	118 <sanitizer>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	119 <valid initial="string.letters,string.digits">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	120 <add value="\|"/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	121 <add value=":"/>
9 d8c2a68643ce planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 8 diff changeset	122 <add value="."/>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	123 </valid>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	124 </sanitizer>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	125 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	126 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	127
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	128 <xml name="smoothLength">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	129 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	130 label="Smooth values using the following length (in bases)"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	131 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	132 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	133
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	134
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	135 <xml name="kmeans_clustering">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	136 <conditional name="used_multiple_regions">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	137 <param name="used_multiple_regions_options" type="select"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	138 label="Did you compute the matrix with more than one groups of regions?"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 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.">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	140 <option value="yes">Yes, I used multiple groups of regions</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	141 <option value="no">No, I used only one group</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	142 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	143 <when value="no">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	144 <conditional name="clustering">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	145 <param name="clustering_options" type="select" label="Clustering algorithm">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	146 <option value="none">No clustering</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	147 <option value="kmeans">Kmeans clustering</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	148 <option value="hclust">Hierarchical clustering</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	149 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	150 <when value="kmeans">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	151 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	152 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	153 This only works for data that is not grouped, otherwise only the first group will be clustered.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	154 If more specific clustering methods are required it is advisable to save the underlying matrix and
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	155 run the clustering using other software."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	156 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	157 <when value="hclust">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	158 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	159 help="WARNING: This option causes the tool to run for a very long time! When this option is
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	160 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	161 This only works for data that is not grouped, otherwise only the first group will be clustered.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	162 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	163 If more specific clustering methods are required it is advisable to save the underlying matrix and
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	164 run the clustering using other software."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	165 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	166 <when value="none" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	167 </conditional>
16 ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	168 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	169 label="Compute the silhouette score for each region"
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	170 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	171 The silhouette score is a measure of how similar a region is to other regions in the same cluster as
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	172 opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	173 The silhouette evaluation can be very slow when you have more than 100 000 regions." />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	174 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	175 <when value="yes" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	176 </conditional>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	177 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	178
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	179 <token name="@KMEANS_CLUSTERING@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	180 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	181 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	182 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	183 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	184 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	185 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	186 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	187 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	188 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	189 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	190 #end if
16 ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	191 $advancedOpt.used_multiple_regions.silhouette
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	192 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	193 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	194
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	195 <xml name="samFlags">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	196 <param argument="--samFlagInclude" type="integer" optional="True" value=""
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	197 label="Include reads based on the SAM flag"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 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."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	199 <param argument="--samFlagExclude" type="integer" optional="True" value=""
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	200 label="Exclude reads based on the SAM flag"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 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."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	202 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	203
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	204 <xml name="fragLength">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	205 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	206 label="Minimum fragment length for inclusion."
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	207 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	208 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	209 label="Maximum fragment length for inclusion."
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	210 help="A value of 0 (the default) is equivalent to no maximum." />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	211 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	212
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	213 <xml name="read_processing_options">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	214 <expand macro="extendReads" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	215 <expand macro="ignoreDuplicates" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	216 <expand macro="centerReads" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	217 <expand macro="minMappingQuality" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	218 <expand macro="samFlags" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	219 <expand macro="fragLength" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	220 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	221
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	222 <xml name="gtf_options">
6 031a98a187c4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c bgruening parents: 5 diff changeset	223 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	224 label="Use a metagene model"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	225 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	226 <param argument="--transcriptID" optional="True" value="transcript" type="text"
11 3909b643c81c planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 10 diff changeset	227 label="transcript designator"
16 ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	228 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	229 <param argument="--exonID" optional="True" value="exon" type="text"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	230 label="exon designator"
16 ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	231 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	232 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	233 label="transcriptID key designator"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	234 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	235 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	236 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	237 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	238 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	239
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	240
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	241 <xml name="plotNumbers">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	242 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	243 label="Plot the correlation value"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	244 help="If set, then the correlation number is plotted on top of the heatmap."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	245 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	246
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	247 <xml name="extendReads">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	248 <conditional name="doExtendCustom">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	249 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	250 help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	251 By default each read mate is extended.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	252 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	253 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	254 Reads are only extended if --extendReads is set to a value greater than the read length. NOTE: For spliced-read data, this option is not
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	255 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	256 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	257 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	258 <option value="custom">A custom length, which will be applied to ALL reads.</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	259 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	260 <when value="no" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	261 <when value="yes" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	262 <when value="custom">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	263 <param name="extendReadsValue" type="integer" value="300" min="1"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	264 label="Extend reads to the given average fragment size"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	265 help="Extend all reads to this length" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	266 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	267 </conditional>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	268 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	269
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	270 <xml name="corMethod">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	271 <param argument="--corMethod" type="select" label="Correlation method">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	272 <option value="spearman" selected="True">Spearman</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	273 <option value="pearson">Pearson</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	274 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	275 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	276
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	277 <xml name="distanceBetweenBins">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	278 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	279 label="Distance between bins"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	280 help="By default, multiBamSummary considers consecutive bins of
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	281 the specified 'Bin size'. However, to reduce the
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	282 computation time, a larger distance between bins can
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	283 be given. Larger distances result in fewer bins being
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	284 considered."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	285 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	286
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	287 <xml name="centerReads">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	288 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	289 label="Center regions with respect to the fragment length"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	290 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	291 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	292
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	293 <xml name="ignoreDuplicates">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	294 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	295 label="Ignore duplicates"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 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." />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	297 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	298
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	299 <xml name="sortUsing">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	300 <param argument="--sortUsing" type="select" label="Method used for sorting"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	301 help="For each row the method is computed.">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	302 <option value="mean" selected="true">mean</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	303 <option value="median">median</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	304 <option value="min">min</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	305 <option value="max">max</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	306 <option value="sum">sum</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	307 <option value="region_length">region length</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	308 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	309 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	310
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	311 <xml name="sortRegionsComputeMatrix">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	312 <param argument="--sortRegions" type="select" label="Sort regions"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 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.">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	314 <option value="no">no ordering</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	315 <option value="keep" selected="true">maintain the same ordering as the input files</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	316 <option value="descend">descending order</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	317 <option value="ascend">ascending order</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	318 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	319 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	320
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	321 <xml name="sortRegions">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	322 <param argument="--sortRegions" type="select" label="Sort regions"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 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.">
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	324 <option value="no">maintain the same ordering as the input files</option>
1 0240a81c3ae6 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 0 diff changeset	325 <option value="descend" selected="true">descending order</option>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	326 <option value="ascend">ascending order</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	327 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	328 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	329
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	330 <xml name="minMappingQuality">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	331 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	332 label="Minimum mapping quality"
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	333 help= "If set, only reads with a mapping quality score at least this high are considered."/>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	334 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	335
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	336 <xml name="skipZeros">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	337 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	338 label ="Skip zeros"
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 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 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	340 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	341
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	342 <xml name="fragmentLength">
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	343 <param argument="--fragmentLength" type="integer" min="1" optional="true"
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	344 label="Fragment length used for the sequencing"
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 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 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	346 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	347
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	348 <xml name="scaleFactor">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	349 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	350 help="The computed scaling factor will be multiplied by this (default 1)." />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	351 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	352
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	353 <xml name="scaleFactors">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	354 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	355 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	356 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	357
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	358 <xml name="stdio">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	359 <stdio>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	360 <exit_code range="1:" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	361 <exit_code range=":-1" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	362 <regex match="Error:" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	363 <regex match="Exception:" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	364 <regex match="EXception:" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	365 <regex match="Traceback" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	366 </stdio>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	367 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	368
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	369 <xml name="pseudocount">
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 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 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	371 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	372 <token name="@REFERENCES@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	373
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	374 .. class:: infomark
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	375
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	376 For more information on the tools, please visit our `help site`_.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	377
16 ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	378 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	379
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 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`_.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	381
16 ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	382 .. _Biostars: http://biostars.org
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	383 .. _on github: http://github.com
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	384 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	385 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	386 .. _help site: https://deeptools.readthedocs.org/
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	387
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	388 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	389 <xml name="citations">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	390 <citations>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	391 <citation type="doi">10.1093/nar/gkw257</citation>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	392 <yield />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	393 </citations>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	394 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	395
4 d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	396 <xml name="multiple_input_bams" tokens="MIN">
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	397 <conditional name="multibam_conditional">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 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.">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	399 <option value="No" selected="true">No</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	400 <option value="Yes">Yes</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	401 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	402 <when value="No">
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	403 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	404 label="BAM/CRAM file" multiple="true"
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	405 help=""/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	406 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	407 <when value="Yes">
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	408 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	409 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	410 </repeat>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	411 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	412 </conditional>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	413 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	414
4 d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	415 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	416 <conditional name="multibigwig_conditional">
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 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
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	418 is vital to you, select Yes below.">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	419 <option value="No" selected="true">No</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	420 <option value="Yes">Yes</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	421 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	422 <when value="No">
4 d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	423 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	424 label="@LABEL@"
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	425 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	426 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	427 <when value="Yes">
4 d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	428 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 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."/>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	430 </repeat>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	431 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	432 </conditional>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	433 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	434
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	435 <xml name="custom_sample_labels">
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	436 <conditional name="custom_sample_labels_conditional">
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 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.">
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	438 <option value="No" selected="true">No, use sample names in the history</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	439 <option value="Yes">Yes, I want to specify new labels</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	440 </param>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	441 <when value="No">
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	442 </when>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	443 <when value="Yes">
20 e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 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')">
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	445 <sanitizer>
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	446 <valid initial="string.letters,string.digits,string.whitespace">
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	447 <add value="'" />
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	448 <add value="_" />
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	449 </valid>
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	450 </sanitizer>
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	451 <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
e6d0bff01239 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412 bgruening parents: 19 diff changeset	452 </param>
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	453 </when>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	454 </conditional>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	455 </xml>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	456
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	457 <xml name="plotTitle">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	458 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	459 label="Title of the plot"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	460 help="Title of the plot, to be printed on top of the generated image." />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	461 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	462
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	463 <xml name="legendLocation">
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	464 <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.">
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	465 <option value="best" selected="true">Best (automatic)</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	466 <option value="upper-right">upper-right</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	467 <option value="upper-left">upper-left</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	468 <option value="upper-center">upper-center</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	469 <option value="lower-right">lower-right</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	470 <option value="lower-left">lower-left</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	471 <option value="lower-center">lower-center</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	472 <option value="center-right">center-right</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	473 <option value="center-left">center-left</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	474 <option value="center">center</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	475 <option value="none">none (only works for heatmaps</option>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	476 </param>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	477 </xml>
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	478
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	479 <xml name="labelRotation">
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	480 <param argument="--labelRotation" type="integer" value="0"
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	481 label="Rotation of the X-axis labels (in degrees)"
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	482 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." />
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	483 </xml>
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	484
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	485
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	486 <token name="@multiple_input_bams@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	487 <![CDATA[
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	488 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
18 7e6bcd2e5128 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5 bgruening parents: 17 diff changeset	489 #set custom_labels=$custom_sample_labels_conditional.labels
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	490 #end if
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	491 #set files=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	492 #set labels=[]
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	493 #import re
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	494 #if $multibam_conditional.orderMatters == "No":
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	495 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	496 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
9 d8c2a68643ce planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 8 diff changeset	497 ln -s '${bamfile}' './${counter}.bam' &&
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	498 #if $bamfile.ext == 'bam':
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	499 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	500 #else:
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	501 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	502 #end if
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	503 #silent $files.append("'%s.bam'" % $counter)
18 7e6bcd2e5128 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5 bgruening parents: 17 diff changeset	504 #silent $labels.append("'%s'" % $identifier)
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	505 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	506 #else:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	507 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	508 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
9 d8c2a68643ce planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 8 diff changeset	509 ln -s '${f.bamfiles}' './${counter}.bam' &&
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	510 #if $f.bamfiles.ext == 'bam':
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	511 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	512 #else:
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	513 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	514 #end if
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	515 #silent $files.append("'%s.bam'" % $counter)
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	516 #silent $labels.append("'%s'" % $identifier)
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	517 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	518 #end if
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	519 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	520 #set labels=custom_labels
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	521 #end if
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	522 ]]>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	523 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	524
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	525 <token name="@multiple_input_bigwigs@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	526 <![CDATA[
13 f98fc5acd9f7 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 12 diff changeset	527 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
18 7e6bcd2e5128 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5 bgruening parents: 17 diff changeset	528 #set custom_labels=$custom_sample_labels_conditional.labels
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	529 #end if
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	530 #set files=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	531 #set labels=[]
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	532 #import re
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	533 #if $multibigwig_conditional.orderMatters == "No":
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	534 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
4 d3ca92396f80 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 bgruening parents: 2 diff changeset	535 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
9 d8c2a68643ce planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 8 diff changeset	536 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	537 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	538 #silent $labels.append("'%s'" % $identifier)
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	539 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	540 #else:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	541 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	542 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
9 d8c2a68643ce planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 8 diff changeset	543 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	544 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
2 000ef7d1b4ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 1 diff changeset	545 #silent $labels.append("'%s'" % $identifier)
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	546 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	547 #end if
13 f98fc5acd9f7 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 12 diff changeset	548 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
12 f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	549 #set labels=custom_labels
f855bc64657a planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 11 diff changeset	550 #end if
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	551 ]]>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	552 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	553
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	554 <xml name="blacklist">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	555 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	556 label="Blacklisted regions in BED/GTF format"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	557 help="One or more files containing regions to exclude from the analysis" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	558 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	559
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	560 <token name="@blacklist@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	561 <![CDATA[
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	562 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	563 #set blfiles=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	564 #for $f in $advancedOpt.blackListFileName:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	565 #silent $blfiles.append("'%s'" % $f)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	566 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	567 #if $blfiles != ["'None'"]:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	568 --blackListFileName #echo ' '.join($blfiles)#
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	569 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	570 #end if
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	571 ]]>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	572 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	573
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	574 <xml name="multiple_bed">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	575 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	576 label="Regions in BED/GTF format"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	577 help="One or more files containing regions to include in the analysis" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	578 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	579
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	580 <token name="@multiple_bed@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	581 <![CDATA[
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	582 #set files=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	583 #set labels=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	584 #for $f in $BED:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	585 #silent $files.append("'%s'" % $f)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	586 #silent $labels.append("'%s'" % $f.display_name)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	587 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	588 #if len($files) > 0:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	589 --BED #echo ' '.join($files)#
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	590 --regionLabels #echo ' '.join($labels)#
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	591 #end if
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	592 ]]>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	593 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	594
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	595 <xml name="reference_genome_source">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	596 <conditional name="source">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	597 <param name="ref_source" type="select" label="Reference genome">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	598 <option value="cached">locally cached</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	599 <option value="history">in your history</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	600 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	601 <when value="cached">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	602 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	603 <options from_data_table="lastz_seqs">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	604 <filter type="sort_by" column="1" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	605 <validator type="no_options" message="No indexes are available." />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	606 </options>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	607 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	608 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	609 <when value="history">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	610 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	611 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	612 </conditional>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	613 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	614
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	615 <token name="@reference_genome_source@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	616 #if $source.ref_source=="history":
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	617 --genome $source.input1
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	618 #else:
9 d8c2a68643ce planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 8 diff changeset	619 --genome '$source.input1_2bit.fields.path'
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	620 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	621 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	622
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	623 <xml name="effectiveGenomeSize">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	624 <conditional name="effectiveGenomeSize">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	625 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	626 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.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	627 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	628 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	629 <option value="93260000">ce10 (93260000)</option>
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	630 <option value="130428560">dm3 (130428560)</option>
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	631 <option value="125464728">dm6 (125464728)</option>
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	632 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	633 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	634 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	635 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	636 <option value="specific">user specified</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	637 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	638 <when value="specific">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	639 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	640 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	641 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	642 <when value="93260000" />
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	643 <when value="130428560" />
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	644 <when value="125464728" />
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	645 <when value="2685511504" />
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	646 <when value="2701495761" />
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	647 <when value="2304947926" />
8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	648 <when value="2308125349" />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	649 </conditional>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	650 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	651
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	652 <xml name="skipNAs">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	653 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	654 label="Ignore missing data?"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	655 help="This parameter determines if non-covered regions
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	656 (regions without overlapping reads) in a bam/bigWig file
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	657 should be skipped. The default is to treat those
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	658 regions as having a value of zero. The decision to
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	659 skip non-covered regions depends on the interpretation
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	660 of the data. Non-covered regions may represent, for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	661 example, repetitive regions that should be ignored.
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	662 (default: False)" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	663 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	664
14 9384cd033f30 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 13 diff changeset	665 <xml name="skipZeroOverZero">
9384cd033f30 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 13 diff changeset	666 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
9384cd033f30 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 13 diff changeset	667 help="Skip bins where BOTH files lack coverage.">
9384cd033f30 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 13 diff changeset	668 <option value="" selected="true">No</option>
9384cd033f30 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 13 diff changeset	669 <option value="--skipZeroOverZero">Yes, skip them.</option>
9384cd033f30 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 13 diff changeset	670 </param>
9384cd033f30 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 13 diff changeset	671 </xml>
9384cd033f30 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 13 diff changeset	672
10 848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	673 <xml name="exactScaling">
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	674 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	675 label="Compute an exact scaling factor"
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	676 help="Compute an exact scaling factor rather than one based on
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	677 sampled reads. This is only useful in cases where you are
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	678 filtering some alignments out AND this are both rare and
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	679 tend to clump together in the genome. In such cases the
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	680 region-based sampling employed by deepTools would produce
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	681 inaccurate scaling factors. Note that this option results
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	682 in the process taking significantly more time to complete." />
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	683 </xml>
848ce8f81e6e planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 9 diff changeset	684
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	685 <xml name="input_save_matrix_values">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	686 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	687 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	688
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	689 <xml name="input_graphic_output_settings">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	690 <conditional name="output" >
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	691 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	692 <option value="no" selected="true">no</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	693 <option value="yes">yes</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	694 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	695 <when value="no" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	696 <when value="yes">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	697 <yield />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	698 <param name="saveSortedRegions" type="boolean"
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	699 argument="--outFileSortedRegions"
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	700 label="Save the regions after skipping zeros or min/max threshold values"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	701 help="The order of the regions in the file follows the sorting order selected. This is useful,
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	702 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	703 </when>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	704 </conditional>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	705 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	706
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	707
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	708 <xml name="input_image_file_format">
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	709 <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 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	710 <option value="png" selected="true">png</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	711 <option value="pdf">pdf</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	712 <option value="svg">svg</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	713 <option value="eps">eps</option>
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	714 <option value="plotly">plotly</option>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	715 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	716 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	717
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	718 <xml name="output_dpi">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	719 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	720 label="Image dpi" help=""/>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	721 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	722
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	723 <xml name="output_image_file_format">
11 3909b643c81c planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 10 diff changeset	724 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	725 <change_format>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	726 <when input="output.outFileFormat" value="pdf" format="pdf" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	727 <when input="output.outFileFormat" value="svg" format="svg" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	728 <when input="output.outFileFormat" value="eps" format="eps" />
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	729 <when input="output.outFileFormat" value="plotly" format="html" />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	730 </change_format>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	731 </data>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	732 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	733
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	734 <xml name="output_image_file_format_not_nested">
11 3909b643c81c planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 10 diff changeset	735 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	736 <change_format>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	737 <when input="outFileFormat" value="pdf" format="pdf" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	738 <when input="outFileFormat" value="svg" format="svg" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	739 <when input="outFileFormat" value="eps" format="eps" />
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	740 <when input="outFileFormat" value="plotly" format="html" />
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	741 </change_format>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	742 </data>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	743 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	744
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	745 <xml name="output_save_matrix_values">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	746 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	747 <filter>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	748 ((
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	749 output['showOutputSettings'] == 'yes' and
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	750 output['saveMatrix'] is True
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	751 ))
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	752 </filter>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	753 </data>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	754 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	755
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	756 <xml name="output_graphic_outputs">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	757 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	758 <filter>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	759 ((
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	760 output['showOutputSettings'] == 'yes' and
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	761 output['saveSortedRegions'] is True
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	762 ))
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	763 </filter>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	764 </data>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	765 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	766
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	767 <xml name="colorMap">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	768 <param name="colorMap" type="select" label="Color map to use for the heatmap"
7 8d191de9b0f5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 6 diff changeset	769 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	770 <option value="RdYlBu" selected="true">RdYlBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	771 <option value="Accent">Accent</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	772 <option value="Spectral">Spectral</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	773 <option value="Set1">Set1</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	774 <option value="Set2">Set2</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	775 <option value="Set3">Set3</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	776 <option value="Dark2">Dark2</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	777 <option value="Reds">Reds</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	778 <option value="Oranges">Oranges</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	779 <option value="Greens">Greens</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	780 <option value="Blues">Blues</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	781 <option value="Greys">Greys</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	782 <option value="Purples">Purples</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	783 <option value="Paired">Paired</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	784 <option value="Pastel1">Pastel1</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	785 <option value="Pastel2">Pastel2</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	786 <option value="spring">spring</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	787 <option value="summer">summer</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	788 <option value="autumn">autumn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	789 <option value="winter">winter</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	790 <option value="hot">hot</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	791 <option value="coolwarm">coolwarm</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	792 <option value="cool">cool</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	793 <option value="seismic">seismic</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	794 <option value="terrain">terrain</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	795 <option value="ocean">ocean</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	796 <option value="rainbow">rainbow</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	797 <option value="bone">bone</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	798 <option value="flag">flag</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	799 <option value="prism">prism</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	800 <option value="cubehelix">cubehelix</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	801 <option value="binary">binary</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	802 <option value="pink">pink</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	803 <option value="gray">gray</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	804 <option value="copper">copper</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	805 <option value="BrBG">BrBG</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	806 <option value="BuGn">BuGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	807 <option value="BuPu">BuPu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	808 <option value="GnBu">GnBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	809 <option value="OrRd">OrRd</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	810 <option value="PiYG">PiYG</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	811 <option value="PRGn">PRGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	812 <option value="PuOr">PuOr</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	813 <option value="PuRd">PuRd</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	814 <option value="PuBu">PuBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	815 <option value="RdBu">RdBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	816 <option value="RdGy">RdGy</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	817 <option value="RdPu">RdPu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	818 <option value="YlGn">YlGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	819 <option value="PuBuGn">PuBuGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	820 <option value="RdYlGn">RdYlGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	821 <option value="YlGnBu">YlGnBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	822 <option value="YlOrBr">YlOrBr</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	823 <option value="YlOrRd">YlOrRd</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	824 <option value="gist_gray">gist_gray</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	825 <option value="gist_stern">gist_stern</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	826 <option value="gist_earth">gist_earth</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	827 <option value="gist_yarg">gist_yarg</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	828 <option value="gist_ncar">gist_ncar</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	829 <option value="gist_rainbow">gist_rainbow</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	830 <option value="gist_heat">gist_heat</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	831 <option value="gnuplot">gnuplot</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	832 <option value="gnuplot2">gnuplot2</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	833 <option value="CMRmap">CMRmap</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	834 <option value="bwr">bwr</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	835 <option value="hsv">hsv</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	836 <option value="brg">brg</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	837 <option value="jet">jet</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	838 <option value="afmhot">afmhot</option>
16 ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	839 <option value="Wistia">Wistia</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	840 <option value="cividis">cividis</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	841 <option value="icefire">icefire</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	842 <option value="inferno">inferno</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	843 <option value="magma">magma</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	844 <option value="mako">mako</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	845 <option value="nipy_spectral">nipy_spectral</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	846 <option value="plasma">plasma</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	847 <option value="rocket">rocket</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	848 <option value="tab10">tab10</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	849 <option value="tab20">tab20</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	850 <option value="tab20b">tab20b</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	851 <option value="tab20c">tab20c</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	852 <option value="twilight">twilight</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	853 <option value="twilight_shifted">twilight_shifted</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	854 <option value="viridis">viridis</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	855 <option value="vlag">vlag</option>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	856 <option value="Accent_r">Accent reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	857 <option value="Spectral_r">Spectral reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	858 <option value="Set1_r">Set1 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	859 <option value="Set2_r">Set2 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	860 <option value="Set3_r">Set3 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	861 <option value="Dark2_r">Dark2 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	862 <option value="Reds_r">Reds reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	863 <option value="Oranges_r">Oranges reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	864 <option value="Greens_r">Greens reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	865 <option value="Blues_r">Blues reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	866 <option value="Greys_r">Greys reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	867 <option value="Purples_r">Purples reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	868 <option value="Paired_r">Paired reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	869 <option value="Pastel1_r">Pastel1 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	870 <option value="Pastel2_r">Pastel2 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	871 <option value="spring_r">spring reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	872 <option value="summer_r">summer reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	873 <option value="autumn_r">autumn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	874 <option value="winter_r">winter reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	875 <option value="hot_r">hot reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	876 <option value="coolwarm_r">coolwarm reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	877 <option value="cool_r">cool reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	878 <option value="seismic_r">seismic reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	879 <option value="terrain_r">terrain reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	880 <option value="ocean_r">ocean reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	881 <option value="rainbow_r">rainbow reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	882 <option value="bone_r">bone reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	883 <option value="flag_r">flag reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	884 <option value="prism_r">prism reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	885 <option value="cubehelix_r">cubehelix reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	886 <option value="binary_r">binary reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	887 <option value="pink_r">pink reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	888 <option value="gray_r">gray reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	889 <option value="copper_r">copper reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	890 <option value="BrBG_r">BrBG reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	891 <option value="BuGn_r">BuGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	892 <option value="BuPu_r">BuPu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	893 <option value="GnBu_r">GnBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	894 <option value="OrRd_r">OrRd reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	895 <option value="PiYG_r">PiYG reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	896 <option value="PRGn_r">PRGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	897 <option value="PuOr_r">PuOr reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	898 <option value="PuRd_r">PuRd reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	899 <option value="PuBu_r">PuBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	900 <option value="RdBu_r">RdBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	901 <option value="RdGy_r">RdGy reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	902 <option value="RdPu_r">RdPu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	903 <option value="YlGn_r">YlGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	904 <option value="PuBuGn_r">PuBuGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	905 <option value="RdYlBu_r">RdYlBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	906 <option value="RdYlGn_r">RdYlGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	907 <option value="YlGnBu_r">YlGnBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	908 <option value="YlOrBr_r">YlOrBr reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	909 <option value="YlOrRd_r">YlOrRd reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	910 <option value="gist_gray_r">gist_gray reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	911 <option value="gist_stern_r">gist_stern reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	912 <option value="gist_earth_r">gist_earth reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	913 <option value="gist_yarg_r">gist_yarg reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	914 <option value="gist_ncar_r">gist_ncar reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	915 <option value="gist_rainbow_r">gist_rainbow reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	916 <option value="gist_heat_r">gist_heat reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	917 <option value="gnuplot_r">gnuplot reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	918 <option value="gnuplot2_r">gnuplot2 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	919 <option value="CMRmap_r">CMRmap reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	920 <option value="bwr_r">bwr reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	921 <option value="hsv_r">hsv reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	922 <option value="brg_r">brg reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	923 <option value="jet_r">jet reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	924 <option value="afmhot_r">afmhot reversed</option>
16 ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	925 <option value="Wistia_r">Wistia reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	926 <option value="cividis_r">cividis reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	927 <option value="icefire_r">icefire reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	928 <option value="inferno_r">inferno reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	929 <option value="magma_r">magma reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	930 <option value="mako_r">mako reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	931 <option value="nipy_spectral_r">nipy_spectral reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	932 <option value="plasma_r">plasma reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	933 <option value="rocket_r">rocket reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	934 <option value="tab10_r">tab10 reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	935 <option value="tab20_r">tab20 reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	936 <option value="tab20b_r">tab20b reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	937 <option value="tab20c_r">tab20c reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	938 <option value="twilight_r">twilight reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	939 <option value="twilight_shifted_r">twilight_shifted reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	940 <option value="viridis_r">viridis reversed</option>
ee3a1b0f45f1 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 15 diff changeset	941 <option value="vlag_r">vlag reversed</option>
0 1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	942 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	943
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	944 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	945
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: diff changeset	946 </macros>

Mercurial > repos > bgruening > deeptools_compute_matrix_operations

annotate deepTools_macros.xml @ 20:e6d0bff01239 draft default tip