deeptools_alignmentsieve: deepTools

annotate deepTools_macros.xml @ 10:e5a296ce8fbb draft

"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"

author	bgruening
date	Fri, 11 Feb 2022 16:01:39 +0000
parents	6531acf8209f
children	d8c919d26d0e

rev	line source
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	1 <macros>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	2
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
10 e5a296ce8fbb "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb" bgruening parents: 9 diff changeset	4 <token name="@WRAPPER_VERSION@">3.5.1.0</token>
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	5 <xml name="requirements">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	6 <requirements>
10 e5a296ce8fbb "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb" bgruening parents: 9 diff changeset	7 <requirement type="package" version="3.5.1">deeptools</requirement>
5 0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	8 <requirement type="package" version="1.9">samtools</requirement>
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	9 </requirements>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	10 <expand macro="stdio" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	11 <version_command>@BINARY@ --version</version_command>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	12 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	13
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	14 <xml name="advancedOpt_scaffold">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	15 <conditional name="advancedOpt">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	16 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	17 <option value="no" selected="true">no</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	18 <option value="yes">yes</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	19 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	20 <when value="no" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	21 <when value="yes">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	22 <yield/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	23 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	24 </conditional>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	25 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	26
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	27 <token name="@PLOTWIDTHHEIGHT@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	28 --plotWidth '$advancedOpt.plotWidth'
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	29 --plotHeight '$advancedOpt.plotHeight'
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	30 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	31
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	32 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	33 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	34 label="Plot height"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	36
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	37 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	38 label="Plot width"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	39 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	40 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	41
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	42 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	43 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	44 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	45 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	46 --extendReads
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	47 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	48 $advancedOpt.ignoreDuplicates
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	49 $advancedOpt.centerReads
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	50 #if $advancedOpt.minMappingQuality:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	51 --minMappingQuality '$advancedOpt.minMappingQuality'
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	52 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	53 #if $advancedOpt.samFlagInclude:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	54 --samFlagInclude $advancedOpt.samFlagInclude
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	55 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	56 #if $advancedOpt.samFlagExclude:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	57 --samFlagExclude $advancedOpt.samFlagExclude
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	58 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	59 #if $advancedOpt.minFragmentLength:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	60 --minFragmentLength $advancedOpt.minFragmentLength
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	61 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	62 #if $advancedOpt.maxFragmentLength:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	63 --maxFragmentLength $advancedOpt.maxFragmentLength
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	64 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	65 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	66
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	67 <token name="@ADVANCED_OPTS_GTF@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	68 $advancedOpt.metagene
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	69 #if $advancedOpt.transcriptID:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	70 --transcriptID $advancedOpt.transcriptID
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	71 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	72 #if $advancedOpt.exonID:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	73 --exonID $advancedOpt.exonID
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	74 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	75 #if $advancedOpt.transcript_id_designator:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	76 --transcript_id_designator $advancedOpt.transcript_id_designator
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	77 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	78 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	79
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	80 <xml name="heatmap_options">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	81 <expand macro="zMin_zMax" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	82 <expand macro="colorMap" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	83 <expand macro="plotTitle" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	84 <expand macro="plotNumbers" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	85 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	86
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	87 <token name="@HEATMAP_OPTIONS@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	88 #if str($plotting_type.zMin) != "":
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	89 --zMin $plotting_type.zMin
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	90 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	91 #if str($plotting_type.zMax) != "":
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	92 --zMax $plotting_type.zMax
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	93 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	94 --colorMap '$plotting_type.colorMap'
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	95 $plotting_type.plotNumbers
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	96 --plotTitle '$plotting_type.plotTitle'
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	97 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	98
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	99
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	100 <xml name="includeZeros">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	101 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	102 label="Include zeros"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	103 help="If set, then regions with zero counts for all BAM/CRAM files are included. The default behavior is to ignore such regions." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	104 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	105
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	106 <xml name="zMin_zMax">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	107 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	108 help="If not specified the value is set automatically."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	109 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	110 help="If not specified the value is set automatically."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	111 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	112
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	113 <xml name="region_limit_operation">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	114 <param argument="--region" type="text" value=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	115 label="Region of the genome to limit the operation to"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	116 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	117 <sanitizer>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	118 <valid initial="string.letters,string.digits">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	119 <add value="\|"/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	120 <add value=":"/>
2 ea8efdcf151f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 1 diff changeset	121 <add value="."/>
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	122 </valid>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	123 </sanitizer>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	124 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	125 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	126
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	127 <xml name="smoothLength">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	128 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	129 label="Smooth values using the following length (in bases)"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	130 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	131 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	132
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	133
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	134 <xml name="kmeans_clustering">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	135 <conditional name="used_multiple_regions">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	136 <param name="used_multiple_regions_options" type="select"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	137 label="Did you compute the matrix with more than one groups of regions?"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	138 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	139 <option value="yes">Yes, I used multiple groups of regions</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	140 <option value="no">No, I used only one group</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	141 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	142 <when value="no">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	143 <conditional name="clustering">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	144 <param name="clustering_options" type="select" label="Clustering algorithm">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	145 <option value="none">No clustering</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	146 <option value="kmeans">Kmeans clustering</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	147 <option value="hclust">Hierarchical clustering</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	148 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	149 <when value="kmeans">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	150 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	151 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	152 This only works for data that is not grouped, otherwise only the first group will be clustered.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	153 If more specific clustering methods are required it is advisable to save the underlying matrix and
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	154 run the clustering using other software."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	155 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	156 <when value="hclust">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	157 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	158 help="WARNING: This option causes the tool to run for a very long time! When this option is
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	159 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	160 This only works for data that is not grouped, otherwise only the first group will be clustered.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	161 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	162 If more specific clustering methods are required it is advisable to save the underlying matrix and
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	163 run the clustering using other software."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	164 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	165 <when value="none" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	166 </conditional>
9 6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	167 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	168 label="Compute the silhouette score for each region"
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	169 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	170 The silhouette score is a measure of how similar a region is to other regions in the same cluster as
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	171 opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	172 The silhouette evaluation can be very slow when you have more than 100 000 regions." />
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	173 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	174 <when value="yes" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	175 </conditional>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	176 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	177
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	178 <token name="@KMEANS_CLUSTERING@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	179 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	180 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	181 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	182 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	183 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	184 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	185 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	186 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	187 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	188 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	189 #end if
9 6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	190 $advancedOpt.used_multiple_regions.silhouette
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	191 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	192 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	193
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	194 <xml name="samFlags">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	195 <param argument="--samFlagInclude" type="integer" optional="True" value=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	196 label="Include reads based on the SAM flag"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	197 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."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	198 <param argument="--samFlagExclude" type="integer" optional="True" value=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	199 label="Exclude reads based on the SAM flag"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	200 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."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	201 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	202
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	203 <xml name="fragLength">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	204 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	205 label="Minimum fragment length for inclusion."
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	206 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	207 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	208 label="Maximum fragment length for inclusion."
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	209 help="A value of 0 (the default) is equivalent to no maximum." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	210 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	211
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	212 <xml name="read_processing_options">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	213 <expand macro="extendReads" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	214 <expand macro="ignoreDuplicates" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	215 <expand macro="centerReads" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	216 <expand macro="minMappingQuality" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	217 <expand macro="samFlags" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	218 <expand macro="fragLength" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	219 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	220
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	221 <xml name="gtf_options">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	222 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	223 label="Use a metagene model"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	224 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." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	225 <param argument="--transcriptID" optional="True" value="transcript" type="text"
4 b2e9d7fbca60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 3 diff changeset	226 label="transcript designator"
9 6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	227 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 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	228 <param argument="--exonID" optional="True" value="exon" type="text"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	229 label="exon designator"
9 6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	230 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 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	231 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	232 label="transcriptID key designator"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	233 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	234 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	235 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	236 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	237 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	238
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	239
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	240 <xml name="plotNumbers">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	241 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	242 label="Plot the correlation value"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	243 help="If set, then the correlation number is plotted on top of the heatmap."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	244 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	245
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	246 <xml name="extendReads">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	247 <conditional name="doExtendCustom">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	248 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	249 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.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	250 By default each read mate is extended.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	251 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	252 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	253 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
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	254 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	255 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	256 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	257 <option value="custom">A custom length, which will be applied to ALL reads.</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	258 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	259 <when value="no" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	260 <when value="yes" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	261 <when value="custom">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	262 <param name="extendReadsValue" type="integer" value="300" min="1"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	263 label="Extend reads to the given average fragment size"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	264 help="Extend all reads to this length" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	265 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	266 </conditional>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	267 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	268
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	269 <xml name="corMethod">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	270 <param argument="--corMethod" type="select" label="Correlation method">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	271 <option value="spearman" selected="True">Spearman</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	272 <option value="pearson">Pearson</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	273 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	274 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	275
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	276 <xml name="distanceBetweenBins">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	277 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	278 label="Distance between bins"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	279 help="By default, multiBamSummary considers consecutive bins of
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	280 the specified 'Bin size'. However, to reduce the
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	281 computation time, a larger distance between bins can
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	282 be given. Larger distances result in fewer bins being
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	283 considered."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	284 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	285
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	286 <xml name="centerReads">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	287 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	288 label="Center regions with respect to the fragment length"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	289 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."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	290 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	291
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	292 <xml name="ignoreDuplicates">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	293 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	294 label="Ignore duplicates"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	295 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." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	296 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	297
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	298 <xml name="sortUsing">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	299 <param argument="--sortUsing" type="select" label="Method used for sorting"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	300 help="For each row the method is computed.">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	301 <option value="mean" selected="true">mean</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	302 <option value="median">median</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	303 <option value="min">min</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	304 <option value="max">max</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	305 <option value="sum">sum</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	306 <option value="region_length">region length</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	307 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	308 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	309
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	310 <xml name="sortRegionsComputeMatrix">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	311 <param argument="--sortRegions" type="select" label="Sort regions"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	312 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	313 <option value="no">no ordering</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	314 <option value="keep" selected="true">maintain the same ordering as the input files</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	315 <option value="descend">descending order</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	316 <option value="ascend">ascending order</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	317 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	318 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	319
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	320 <xml name="sortRegions">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	321 <param argument="--sortRegions" type="select" label="Sort regions"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	322 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	323 <option value="no">maintain the same ordering as the input files</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	324 <option value="descend" selected="true">descending order</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	325 <option value="ascend">ascending order</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	326 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	327 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	328
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	329 <xml name="minMappingQuality">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	330 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	331 label="Minimum mapping quality"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	332 help= "If set, only reads with a mapping quality score at least this high are considered."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	333 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	334
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	335 <xml name="skipZeros">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	336 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	337 label ="Skip zeros"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	338 help ="If set, then zero counts that happen for all BAM/CRAM files given are ignored. This may result in fewer considered regions." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	339 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	340
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	341 <xml name="fragmentLength">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	342 <param argument="--fragmentLength" type="integer" min="1" optional="true"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	343 label="Fragment length used for the sequencing"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	344 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."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	345 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	346
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	347 <xml name="scaleFactor">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	348 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	349 help="The computed scaling factor will be multiplied by this (default 1)." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	350 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	351
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	352 <xml name="scaleFactors">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	353 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	354 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	355 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	356
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	357 <xml name="stdio">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	358 <stdio>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	359 <exit_code range="1:" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	360 <exit_code range=":-1" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	361 <regex match="Error:" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	362 <regex match="Exception:" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	363 <regex match="EXception:" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	364 <regex match="Traceback" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	365 </stdio>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	366 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	367
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	368 <xml name="pseudocount">
5 0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	369 <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 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	370 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	371
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	372 <token name="@REFERENCES@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	373
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	374 .. class:: infomark
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	375
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	376 For more information on the tools, please visit our `help site`_.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	377
9 6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	378 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	379
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	380 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	381
9 6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	382 .. _Biostars: http://biostars.org
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	383 .. _on github: http://github.com
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	384 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	385 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	386 .. _help site: https://deeptools.readthedocs.org/
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	387
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	388 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	389 <xml name="citations">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	390 <citations>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	391 <citation type="doi">10.1093/nar/gkw257</citation>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	392 <yield />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	393 </citations>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	394 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	395
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	396 <xml name="multiple_input_bams" tokens="MIN">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	397 <conditional name="multibam_conditional">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty 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.">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	399 <option value="No" selected="true">No</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	400 <option value="Yes">Yes</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	401 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	402 <when value="No">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	403 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	404 label="BAM/CRAM file" multiple="true"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	405 help=""/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	406 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	407 <when value="Yes">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	408 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	409 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	410 </repeat>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	411 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	412 </conditional>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	413 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	414
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	415 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	416 <conditional name="multibigwig_conditional">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 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
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	418 is vital to you, select Yes below.">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	419 <option value="No" selected="true">No</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	420 <option value="Yes">Yes</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	421 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	422 <when value="No">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	423 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	424 label="@LABEL@"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	425 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	426 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	427 <when value="Yes">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	428 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: 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."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	430 </repeat>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	431 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	432 </conditional>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	433 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	434
5 0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	435 <xml name="custom_sample_labels">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	436 <conditional name="custom_sample_labels_conditional">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 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.">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	438 <option value="No" selected="true">No, use sample names in the history</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	439 <option value="Yes">Yes, I want to specify new labels</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	440 </param>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	441 <when value="No">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	442 </when>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	443 <when value="Yes">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 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")">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	445 <sanitizer>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	446 <valid initial="string.printable">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	447 </valid>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	448 </sanitizer>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	449 </param>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	450 </when>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	451 </conditional>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	452 </xml>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	453
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	454 <xml name="plotTitle">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	455 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	456 label="Title of the plot"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	457 help="Title of the plot, to be printed on top of the generated image." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	458 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	459
5 0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	460 <xml name="legendLocation">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	461 <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	462 <option value="best" selected="true">Best (automatic)</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	463 <option value="upper-right">upper-right</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	464 <option value="upper-left">upper-left</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	465 <option value="upper-center">upper-center</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	466 <option value="lower-right">lower-right</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	467 <option value="lower-left">lower-left</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	468 <option value="lower-center">lower-center</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	469 <option value="center-right">center-right</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	470 <option value="center-left">center-left</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	471 <option value="center">center</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	472 <option value="none">none (only works for heatmaps</option>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	473 </param>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	474 </xml>
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	475
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	476 <xml name="labelRotation">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	477 <param argument="--labelRotation" type="integer" value="0"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	478 label="Rotation of the X-axis labels (in degrees)"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	479 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	480 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	481
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	482
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	483 <token name="@multiple_input_bams@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	484 <![CDATA[
5 0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	486 #set custom_labels=labels
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	487 #end if
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	488 #set files=[]
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	489 #set labels=[]
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	490 #import re
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	491 #if $multibam_conditional.orderMatters == "No":
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	492 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	493 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
2 ea8efdcf151f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 1 diff changeset	494 ln -s '${bamfile}' './${counter}.bam' &&
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	495 #if $bamfile.ext == 'bam':
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	497 #else:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	499 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	500 #silent $files.append("'%s.bam'" % $counter)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	501 #silent $labels.append("'%s'" % identifier)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	502 #end for
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	503 #else:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	504 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
2 ea8efdcf151f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 1 diff changeset	506 ln -s '${f.bamfiles}' './${counter}.bam' &&
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	507 #if $f.bamfiles.ext == 'bam':
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	508 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	509 #else:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	510 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	511 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	512 #silent $files.append("'%s.bam'" % $counter)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	513 #silent $labels.append("'%s'" % $identifier)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	514 #end for
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	515 #end if
5 0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	516 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	517 #set labels=custom_labels
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	518 #end if
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	519 ]]>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	520 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	521
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	522 <token name="@multiple_input_bigwigs@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	523 <![CDATA[
6 23037a2faf32 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 5 diff changeset	524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
5 0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	525 #set custom_labels=labels
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	526 #end if
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	527 #set files=[]
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	528 #set labels=[]
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	529 #import re
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	530 #if $multibigwig_conditional.orderMatters == "No":
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	531 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	532 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
2 ea8efdcf151f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 1 diff changeset	533 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	534 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	535 #silent $labels.append("'%s'" % $identifier)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	536 #end for
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	537 #else:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	538 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	539 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
2 ea8efdcf151f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 1 diff changeset	540 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	541 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	542 #silent $labels.append("'%s'" % $identifier)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	543 #end for
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	544 #end if
6 23037a2faf32 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf bgruening parents: 5 diff changeset	545 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
5 0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	546 #set labels=custom_labels
0bac1f03ef5d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d bgruening parents: 4 diff changeset	547 #end if
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	548 ]]>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	549 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	550
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	551 <xml name="blacklist">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	552 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	553 label="Blacklisted regions in BED/GTF format"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	554 help="One or more files containing regions to exclude from the analysis" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	555 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	556
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	557 <token name="@blacklist@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	558 <![CDATA[
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	559 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	560 #set blfiles=[]
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	561 #for $f in $advancedOpt.blackListFileName:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	562 #silent $blfiles.append("'%s'" % $f)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	563 #end for
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	564 #if $blfiles != ["'None'"]:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	565 --blackListFileName #echo ' '.join($blfiles)#
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	566 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	567 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	568 ]]>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	569 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	570
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	571 <xml name="multiple_bed">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	572 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	573 label="Regions in BED/GTF format"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	574 help="One or more files containing regions to include in the analysis" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	575 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	576
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	577 <token name="@multiple_bed@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	578 <![CDATA[
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	579 #set files=[]
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	580 #set labels=[]
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	581 #for $f in $BED:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	582 #silent $files.append("'%s'" % $f)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	583 #silent $labels.append("'%s'" % $f.display_name)
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	584 #end for
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	585 #if len($files) > 0:
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	586 --BED #echo ' '.join($files)#
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	587 --regionLabels #echo ' '.join($labels)#
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	588 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	589 ]]>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	590 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	591
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	592 <xml name="reference_genome_source">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	593 <conditional name="source">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	594 <param name="ref_source" type="select" label="Reference genome">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	595 <option value="cached">locally cached</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	596 <option value="history">in your history</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	597 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	598 <when value="cached">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	599 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	600 <options from_data_table="lastz_seqs">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	601 <filter type="sort_by" column="1" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	602 <validator type="no_options" message="No indexes are available." />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	603 </options>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	604 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	605 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	606 <when value="history">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	607 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	608 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	609 </conditional>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	610 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	611
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	612 <token name="@reference_genome_source@">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	613 #if $source.ref_source=="history":
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	614 --genome $source.input1
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	615 #else:
2 ea8efdcf151f planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754 bgruening parents: 1 diff changeset	616 --genome '$source.input1_2bit.fields.path'
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	617 #end if
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	618 </token>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	619
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	620 <xml name="effectiveGenomeSize">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	621 <conditional name="effectiveGenomeSize">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	622 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	623 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	624 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	625 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	626 <option value="93260000">ce10 (93260000)</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	627 <option value="130428560">dm3 (130428560)</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	628 <option value="125464728">dm6 (125464728)</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	629 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	630 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	631 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	632 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	633 <option value="specific">user specified</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	634 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	635 <when value="specific">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	636 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	637 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	638 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	639 <when value="93260000" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	640 <when value="130428560" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	641 <when value="125464728" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	642 <when value="2685511504" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	643 <when value="2701495761" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	644 <when value="2304947926" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	645 <when value="2308125349" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	646 </conditional>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	647 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	648
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	649 <xml name="skipNAs">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	650 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	651 label="Ignore missing data?"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	652 help="This parameter determines if non-covered regions
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	653 (regions without overlapping reads) in a bam/bigWig file
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	654 should be skipped. The default is to treat those
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	655 regions as having a value of zero. The decision to
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	656 skip non-covered regions depends on the interpretation
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	657 of the data. Non-covered regions may represent, for
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	658 example, repetitive regions that should be ignored.
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	659 (default: False)" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	660 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	661
7 81cb13ee2fb8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 6 diff changeset	662 <xml name="skipZeroOverZero">
81cb13ee2fb8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 6 diff changeset	663 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
81cb13ee2fb8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 6 diff changeset	664 help="Skip bins where BOTH files lack coverage.">
81cb13ee2fb8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 6 diff changeset	665 <option value="" selected="true">No</option>
81cb13ee2fb8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 6 diff changeset	666 <option value="--skipZeroOverZero">Yes, skip them.</option>
81cb13ee2fb8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 6 diff changeset	667 </param>
81cb13ee2fb8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 6 diff changeset	668 </xml>
81cb13ee2fb8 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6f68c67a609ee0ee720f7c6e197fe37ecd940b57 bgruening parents: 6 diff changeset	669
3 11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	670 <xml name="exactScaling">
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	671 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	672 label="Compute an exact scaling factor"
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	673 help="Compute an exact scaling factor rather than one based on
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	674 sampled reads. This is only useful in cases where you are
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	675 filtering some alignments out AND this are both rare and
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	676 tend to clump together in the genome. In such cases the
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	677 region-based sampling employed by deepTools would produce
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	678 inaccurate scaling factors. Note that this option results
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	679 in the process taking significantly more time to complete." />
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	680 </xml>
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb bgruening parents: 2 diff changeset	681
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	682 <xml name="input_save_matrix_values">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	683 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	684 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	685
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	686 <xml name="input_graphic_output_settings">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	687 <conditional name="output" >
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	688 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	689 <option value="no" selected="true">no</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	690 <option value="yes">yes</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	691 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	692 <when value="no" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	693 <when value="yes">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	694 <yield />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	695 <param name="saveSortedRegions" type="boolean"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	696 argument="--outFileSortedRegions"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	697 label="Save the regions after skipping zeros or min/max threshold values"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	698 help="The order of the regions in the file follows the sorting order selected. This is useful,
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	699 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	700 </when>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	701 </conditional>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	702 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	703
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	704
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	705 <xml name="input_image_file_format">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	706 <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	707 <option value="png" selected="true">png</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	708 <option value="pdf">pdf</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	709 <option value="svg">svg</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	710 <option value="eps">eps</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	711 <option value="plotly">plotly</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	712 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	713 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	714
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	715 <xml name="output_dpi">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	716 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	717 label="Image dpi" help=""/>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	718 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	719
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	720 <xml name="output_image_file_format">
4 b2e9d7fbca60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 3 diff changeset	721 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	722 <change_format>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	723 <when input="output.outFileFormat" value="pdf" format="pdf" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	724 <when input="output.outFileFormat" value="svg" format="svg" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	725 <when input="output.outFileFormat" value="eps" format="eps" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	726 <when input="output.outFileFormat" value="plotly" format="html" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	727 </change_format>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	728 </data>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	729 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	730
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	731 <xml name="output_image_file_format_not_nested">
4 b2e9d7fbca60 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a bgruening parents: 3 diff changeset	732 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	733 <change_format>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	734 <when input="outFileFormat" value="pdf" format="pdf" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	735 <when input="outFileFormat" value="svg" format="svg" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	736 <when input="outFileFormat" value="eps" format="eps" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	737 <when input="outFileFormat" value="plotly" format="html" />
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	738 </change_format>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	739 </data>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	740 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	741
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	742 <xml name="output_save_matrix_values">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	743 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	744 <filter>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	745 ((
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	746 output['showOutputSettings'] == 'yes' and
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	747 output['saveMatrix'] is True
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	748 ))
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	749 </filter>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	750 </data>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	751 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	752
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	753 <xml name="output_graphic_outputs">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	754 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	755 <filter>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	756 ((
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	757 output['showOutputSettings'] == 'yes' and
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	758 output['saveSortedRegions'] is True
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	759 ))
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	760 </filter>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	761 </data>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	762 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	763
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	764 <xml name="colorMap">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	765 <param name="colorMap" type="select" label="Color map to use for the heatmap"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	766 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	767 <option value="RdYlBu" selected="true">RdYlBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	768 <option value="Accent">Accent</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	769 <option value="Spectral">Spectral</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	770 <option value="Set1">Set1</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	771 <option value="Set2">Set2</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	772 <option value="Set3">Set3</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	773 <option value="Dark2">Dark2</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	774 <option value="Reds">Reds</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	775 <option value="Oranges">Oranges</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	776 <option value="Greens">Greens</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	777 <option value="Blues">Blues</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	778 <option value="Greys">Greys</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	779 <option value="Purples">Purples</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	780 <option value="Paired">Paired</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	781 <option value="Pastel1">Pastel1</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	782 <option value="Pastel2">Pastel2</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	783 <option value="spring">spring</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	784 <option value="summer">summer</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	785 <option value="autumn">autumn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	786 <option value="winter">winter</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	787 <option value="hot">hot</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	788 <option value="coolwarm">coolwarm</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	789 <option value="cool">cool</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	790 <option value="seismic">seismic</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	791 <option value="terrain">terrain</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	792 <option value="ocean">ocean</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	793 <option value="rainbow">rainbow</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	794 <option value="bone">bone</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	795 <option value="flag">flag</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	796 <option value="prism">prism</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	797 <option value="cubehelix">cubehelix</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	798 <option value="binary">binary</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	799 <option value="pink">pink</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	800 <option value="gray">gray</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	801 <option value="copper">copper</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	802 <option value="BrBG">BrBG</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	803 <option value="BuGn">BuGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	804 <option value="BuPu">BuPu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	805 <option value="GnBu">GnBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	806 <option value="OrRd">OrRd</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	807 <option value="PiYG">PiYG</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	808 <option value="PRGn">PRGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	809 <option value="PuOr">PuOr</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	810 <option value="PuRd">PuRd</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	811 <option value="PuBu">PuBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	812 <option value="RdBu">RdBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	813 <option value="RdGy">RdGy</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	814 <option value="RdPu">RdPu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	815 <option value="YlGn">YlGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	816 <option value="PuBuGn">PuBuGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	817 <option value="RdYlGn">RdYlGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	818 <option value="YlGnBu">YlGnBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	819 <option value="YlOrBr">YlOrBr</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	820 <option value="YlOrRd">YlOrRd</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	821 <option value="gist_gray">gist_gray</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	822 <option value="gist_stern">gist_stern</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	823 <option value="gist_earth">gist_earth</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	824 <option value="gist_yarg">gist_yarg</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	825 <option value="gist_ncar">gist_ncar</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	826 <option value="gist_rainbow">gist_rainbow</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	827 <option value="gist_heat">gist_heat</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	828 <option value="gnuplot">gnuplot</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	829 <option value="gnuplot2">gnuplot2</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	830 <option value="CMRmap">CMRmap</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	831 <option value="bwr">bwr</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	832 <option value="hsv">hsv</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	833 <option value="brg">brg</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	834 <option value="jet">jet</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	835 <option value="afmhot">afmhot</option>
9 6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	836 <option value="Wistia">Wistia</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	837 <option value="cividis">cividis</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	838 <option value="icefire">icefire</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	839 <option value="inferno">inferno</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	840 <option value="magma">magma</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	841 <option value="mako">mako</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	842 <option value="nipy_spectral">nipy_spectral</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	843 <option value="plasma">plasma</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	844 <option value="rocket">rocket</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	845 <option value="tab10">tab10</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	846 <option value="tab20">tab20</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	847 <option value="tab20b">tab20b</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	848 <option value="tab20c">tab20c</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	849 <option value="twilight">twilight</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	850 <option value="twilight_shifted">twilight_shifted</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	851 <option value="viridis">viridis</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	852 <option value="vlag">vlag</option>
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	853 <option value="Accent_r">Accent reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	854 <option value="Spectral_r">Spectral reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	855 <option value="Set1_r">Set1 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	856 <option value="Set2_r">Set2 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	857 <option value="Set3_r">Set3 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	858 <option value="Dark2_r">Dark2 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	859 <option value="Reds_r">Reds reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	860 <option value="Oranges_r">Oranges reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	861 <option value="Greens_r">Greens reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	862 <option value="Blues_r">Blues reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	863 <option value="Greys_r">Greys reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	864 <option value="Purples_r">Purples reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	865 <option value="Paired_r">Paired reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	866 <option value="Pastel1_r">Pastel1 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	867 <option value="Pastel2_r">Pastel2 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	868 <option value="spring_r">spring reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	869 <option value="summer_r">summer reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	870 <option value="autumn_r">autumn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	871 <option value="winter_r">winter reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	872 <option value="hot_r">hot reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	873 <option value="coolwarm_r">coolwarm reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	874 <option value="cool_r">cool reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	875 <option value="seismic_r">seismic reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	876 <option value="terrain_r">terrain reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	877 <option value="ocean_r">ocean reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	878 <option value="rainbow_r">rainbow reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	879 <option value="bone_r">bone reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	880 <option value="flag_r">flag reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	881 <option value="prism_r">prism reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	882 <option value="cubehelix_r">cubehelix reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	883 <option value="binary_r">binary reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	884 <option value="pink_r">pink reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	885 <option value="gray_r">gray reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	886 <option value="copper_r">copper reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	887 <option value="BrBG_r">BrBG reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	888 <option value="BuGn_r">BuGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	889 <option value="BuPu_r">BuPu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	890 <option value="GnBu_r">GnBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	891 <option value="OrRd_r">OrRd reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	892 <option value="PiYG_r">PiYG reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	893 <option value="PRGn_r">PRGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	894 <option value="PuOr_r">PuOr reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	895 <option value="PuRd_r">PuRd reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	896 <option value="PuBu_r">PuBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	897 <option value="RdBu_r">RdBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	898 <option value="RdGy_r">RdGy reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	899 <option value="RdPu_r">RdPu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	900 <option value="YlGn_r">YlGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	901 <option value="PuBuGn_r">PuBuGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	902 <option value="RdYlBu_r">RdYlBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	903 <option value="RdYlGn_r">RdYlGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	904 <option value="YlGnBu_r">YlGnBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	905 <option value="YlOrBr_r">YlOrBr reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	906 <option value="YlOrRd_r">YlOrRd reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	907 <option value="gist_gray_r">gist_gray reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	908 <option value="gist_stern_r">gist_stern reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	909 <option value="gist_earth_r">gist_earth reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	910 <option value="gist_yarg_r">gist_yarg reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	911 <option value="gist_ncar_r">gist_ncar reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	912 <option value="gist_rainbow_r">gist_rainbow reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	913 <option value="gist_heat_r">gist_heat reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	914 <option value="gnuplot_r">gnuplot reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	915 <option value="gnuplot2_r">gnuplot2 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	916 <option value="CMRmap_r">CMRmap reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	917 <option value="bwr_r">bwr reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	918 <option value="hsv_r">hsv reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	919 <option value="brg_r">brg reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	920 <option value="jet_r">jet reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	921 <option value="afmhot_r">afmhot reversed</option>
9 6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	922 <option value="Wistia_r">Wistia reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	923 <option value="cividis_r">cividis reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	924 <option value="icefire_r">icefire reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	925 <option value="inferno_r">inferno reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	926 <option value="magma_r">magma reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	927 <option value="mako_r">mako reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	928 <option value="nipy_spectral_r">nipy_spectral reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	929 <option value="plasma_r">plasma reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	930 <option value="rocket_r">rocket reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	931 <option value="tab10_r">tab10 reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	932 <option value="tab20_r">tab20 reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	933 <option value="tab20b_r">tab20b reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	934 <option value="tab20c_r">tab20c reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	935 <option value="twilight_r">twilight reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	936 <option value="twilight_shifted_r">twilight_shifted reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	937 <option value="viridis_r">viridis reversed</option>
6531acf8209f "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef" bgruening parents: 8 diff changeset	938 <option value="vlag_r">vlag reversed</option>
0 dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	939 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	940
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	941 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	942
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty bgruening parents: diff changeset	943 </macros>

Mercurial > repos > bgruening > deeptools_alignmentsieve

annotate deepTools_macros.xml @ 10:e5a296ce8fbb draft