deeptools_bam_coverage: deepTools_macros.xml.orig annotate

annotate deepTools_macros.xml.orig @ 20:eab93a5553ec draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3ea8716dd65a9abde96b69610be31571e4f0ae6d

author	bgruening
date	Fri, 13 May 2016 17:13:52 -0400
parents	892146aaf356
children

rev	line source
13 892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	1 <macros>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	2
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	3 <xml name="advancedOpt_scaffold">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	4 <conditional name="advancedOpt">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	6 <option value="no" selected="true">no</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	7 <option value="yes">yes</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	8 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	9 <when value="no" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	10 <when value="yes">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	11 <yield/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	12 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	13 </conditional>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	14 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	15
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	20 --extendReads
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	21 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	23 $advancedOpt.centerReads
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	26 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	29 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	32 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	33 </token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	34
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	35 <xml name="heatmap_options">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	36 <expand macro="zMin_zMax" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	37 <expand macro="colorMap" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	38 <expand macro="plotTitle" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	39 <expand macro="plotNumbers" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	40 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	41
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	42 <token name="@HEATMAP_OPTIONS@">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	43 #if str($plotting_type.zMin) != "":
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	44 --zMin $plotting_type.zMin
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	45 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	46 #if str($plotting_type.zMax) != "":
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	47 --zMax $plotting_type.zMax
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	48 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	49 --colorMap '$plotting_type.colorMap'
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	50 $plotting_type.plotNumbers
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	51 --plotTitle '$plotting_type.plotTitle'
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	52 </token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	53
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	54
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	55 <xml name="includeZeros">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	57 label="Include zeros"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	58 help="If set, then regions with zero counts for all BAM files are included. The default behavior is to ignore such regions." />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	59 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	60
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	61 <xml name="zMin_zMax">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	63 help="If not specified the value is set automatically."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	65 help="If not specified the value is set automatically."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	66 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	67
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	68 <xml name="region_limit_operation">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	69 <param argument="--region" type="text" value=""
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	70 label="Region of the genome to limit the operation to"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	71 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"." />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	72 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	73
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	75 <<<<<<< HEAD
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	76 <token name="@WRAPPER_VERSION@">2.0.1.0</token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	77 =======
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	78 <token name="@WRAPPER_VERSION@">2.1.0</token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	79 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	80 <xml name="requirements">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	81 <requirements>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	82 <requirement type="package" version="2.7.10">python</requirement>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	83 <requirement type="binary">@BINARY@</requirement>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	84 <<<<<<< HEAD
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	85 <requirement type="package" version="2.0.1">deepTools</requirement>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	86 =======
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	87 <requirement type="package" version="2.1.0">deepTools</requirement>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	88 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	89 <yield />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	90 </requirements>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	91 <expand macro="stdio" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	92 <version_command>@BINARY@ --version</version_command>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	93 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	94
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	95 <xml name="smoothLength">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	96 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	97 label="Smooth values using the following length (in bases)"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	98 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."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	99 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	100
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	101
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	102 <xml name="kmeans_clustering">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	103 <conditional name="used_multiple_regions">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	104 <param name="used_multiple_regions_options" type="select"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	105 label="Did you compute the matrix with more than one groups of regions?"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	106 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.">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	107 <option value="yes">Yes, I used multiple groups of regions</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	108 <option value="no">No, I used only one group</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	109 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	110 <when value="no">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	111 <conditional name="clustering">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	112 <param name="clustering_options" type="select" label="Clustering algorithm">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	113 <option value="none">No clustering</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	114 <option value="kmeans">Kmeans clustering</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	115 <option value="hclust">Hierarchical clustering</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	116 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	117 <when value="kmeans">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	118 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	119 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	120 This only works for data that is not grouped, otherwise only the first group will be clustered.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	121 If more specific clustering methods are required it is advisable to save the underlying matrix and
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	122 run the clustering using other software."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	123 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	124 <when value="hclust">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	125 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	126 help="WARNING: This option causes the tool to run for a very long time! When this option is
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	127 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	128 This only works for data that is not grouped, otherwise only the first group will be clustered.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	129 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	130 If more specific clustering methods are required it is advisable to save the underlying matrix and
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	131 run the clustering using other software."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	132 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	133 <when value="none" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	134 </conditional>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	135 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	136 <when value="yes" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	137 </conditional>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	138 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	139
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	140 <token name="@KMEANS_CLUSTERING@">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	141 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	142 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	143 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	144 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	145 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	146 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	147 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	148 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	149 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	150 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	151 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	152 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	153 </token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	154
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	155 <xml name="samFlags">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	156 <param argument="--samFlagInclude" type="integer" optional="True" value=""
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	157 label="Include reads based on the SAM flag"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	158 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."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	159 <param argument="--samFlagExclude" type="integer" optional="True" value=""
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	160 label="Exclude reads based on the SAM flag"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	161 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."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	162 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	163
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	164 <xml name="read_processing_options">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	165 <expand macro="extendReads" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	166 <expand macro="ignoreDuplicates" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	167 <expand macro="centerReads" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	168 <expand macro="minMappingQuality" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	169 <expand macro="samFlags" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	170 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	171
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	172 <xml name="plotNumbers">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	173 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	174 label="Plot the correlation value"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	175 help="If set, then the correlation number is plotted on top of the heatmap."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	176 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	177
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	178 <xml name="extendReads">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	179 <conditional name="doExtendCustom">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	180 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	181 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	182 By default each read mate is extended.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	183 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	184 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	185 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
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	186 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	187 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	188 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	189 <option value="custom">A custom length, which will be applied to ALL reads.</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	190 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	191 <when value="no" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	192 <when value="yes" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	193 <when value="custom">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	194 <param name="extendReadsValue" type="integer" value="300" min="1"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	195 label="Extend reads to the given average fragment size"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	196 help="Extend all reads to this length" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	197 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	198 </conditional>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	199 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	200
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	201 <xml name="corMethod">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	202 <param argument="--corMethod" type="select" label="Correlation method">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	203 <option value="spearman" selected="True">Spearman</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	204 <option value="pearson">Pearson</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	205 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	206 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	207
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	208 <xml name="distanceBetweenBins">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	209 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	210 label="Distance between bins"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	211 help="By default, multiBamSummary considers consecutive bins of
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	212 the specified 'Bin size'. However, to reduce the
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	213 computation time, a larger distance between bins can
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	214 be given. Larger distances result in fewer bins being
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	215 considered."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	216 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	217
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	218 <xml name="centerReads">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	219 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	220 label="Center regions with respect to the fragment length"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	221 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."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	222 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	223
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	224 <xml name="ignoreDuplicates">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	225 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	226 label="Ignore duplicates"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	227 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." />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	228 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	229
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	230 <xml name="sortUsing">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	231 <param argument="--sortUsing" type="select" label="Method used for sorting"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	232 help="For each row the method is computed.">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	233 <option value="mean" selected="true">mean</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	234 <option value="median">median</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	235 <option value="min">min</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	236 <option value="max">max</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	237 <option value="sum">sum</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	238 <option value="region_length">region length</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	239 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	240 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	241
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	242 <xml name="sortRegions">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	243 <param argument="--sortRegions" type="select" label="Sort regions"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	244 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	245 <option value="no">no ordering</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	246 <option value="descend" selected="true">descending order</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	247 <option value="ascend">ascending order</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	248 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	249 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	250
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	251 <xml name="minMappingQuality">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	252 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	253 label="Minimum mapping quality"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	254 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	255 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	256
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	257 <xml name="skipZeros">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	258 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	259 label ="Skip zeros"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	260 help ="If set, then zero counts that happen for all BAM files given are ignored. This may result in fewer considered regions." />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	261 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	262
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	263 <xml name="fragmentLength">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	264 <param argument="--fragmentLength" type="integer" value="300" min="1"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	265 label="Fragment length used for the sequencing"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	266 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	267 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	268
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	269 <xml name="scaleFactor">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	270 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	271 help="When used in combination with --normalizeTo1x or
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	272 --normalizeUsingRPKM, the computed scaling factor will
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	273 be multiplied by the given scale factor." />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	274 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	275
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	276 <xml name="scaleFactors">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	277 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	278 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	279 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	280
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	281 <xml name="stdio">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	282 <stdio>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	283 <exit_code range="1:" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	284 <exit_code range=":-1" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	285 <regex match="Error:" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	286 <regex match="Exception:" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	287 <regex match="EXception:" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	288 <regex match="Traceback" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	289 </stdio>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	290 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	291
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	292 <xml name="pseudocount">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	293 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	294 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	295
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	296 <token name="@REFERENCES@">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	297
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	298 .. class:: infomark
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	299
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	300 For more information on the tools, please visit our `help site`_.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	301
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	302 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	303
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	304 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	305
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	306 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	307 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	308 .. _help site: https://deeptools.readthedocs.org/
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	309
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	310 </token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	311 <xml name="citations">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	312 <citations>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	313 <citation type="doi">10.1093/nar/gku365</citation>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	314 <yield />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	315 </citations>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	316 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	317
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	318 <xml name="multiple_input_bams">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	319 <param argument="--bamfiles" type="data" format="bam" min="2"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	320 label="Bam file" multiple="true"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	321 help="The BAM file must be sorted."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	322 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	323
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	324 <xml name="multiple_input_bigwigs">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	325 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	326 label="Bigwig file"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	327 help="A Bigwig file."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	328 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	329
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	330 <xml name="plotTitle">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	331 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	332 label="Title of the plot"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	333 help="Title of the plot, to be printed on top of the generated image." />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	334 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	335
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	336
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	337 <token name="@multiple_input_bams@">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	338 <![CDATA[
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	339 #set files=[]
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	340 #set labels=[]
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	341 #for $counter, $bamfile in enumerate($bamfiles):
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	342 ln -s "${bamfile}" "./${counter}.bam" &&
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	343 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	344 #silent $files.append('%s.bam' % $counter)
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	345 #silent $labels.append('%s' % ($bamfile.display_name))
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	346 #end for
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	347 ]]>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	348 </token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	349
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	350 <token name="@multiple_input_bigwigs@">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	351 <![CDATA[
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	352 #set files=[]
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	353 #set labels=[]
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	354 #for $counter, $bigwig in enumerate($bigwigfiles):
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	355 ln -s "${bigwig}" "${counter}.bw" &&
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	356 #silent $files.append('%s.bw' % $counter)
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	357 #silent $labels.append('%s' % ($bigwig.display_name))
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	358 #end for
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	359 ]]>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	360 </token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	361
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	362 <xml name="reference_genome_source">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	363 <conditional name="source">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	364 <param name="ref_source" type="select" label="Reference genome">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	365 <option value="cached">locally cached</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	366 <option value="history">in your history</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	367 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	368 <when value="cached">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	369 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	370 <options from_data_table="lastz_seqs">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	371 <filter type="sort_by" column="1" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	372 <validator type="no_options" message="No indexes are available." />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	373 </options>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	374 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	375 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	376 <when value="history">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	377 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	378 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	379 </conditional>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	380 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	381
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	382 <token name="@reference_genome_source@">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	383 #if $source.ref_source=="history":
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	384 --genome $source.input1
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	385 #else:
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	386 --genome "$source.input1_2bit.fields.path"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	387 #end if
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	388 </token>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	389
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	390 <xml name="effectiveGenomeSize">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	391 <conditional name="effectiveGenomeSize">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	392 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	393 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.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	394 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	395 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	396 <option value="93260000">ce10 (93260000)</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	397 <option value="121400000">dm3 (121400000)</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	398 <option value="2451960000" selected="true">hg19 (2451960000)</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	399 <option value="2150570000">mm9 (2150570000)</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	400 <option value="specific">user specified</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	401 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	402 <when value="specific">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	403 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	404 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	405 <when value="2150570000" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	406 <when value="2451960000" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	407 <when value="121400000" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	408 <when value="93260000" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	409 </conditional>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	410 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	411
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	412 <xml name="skipNAs">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	413 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	414 label="Ignore missing data?"
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	415 help="This parameter determines if non-covered regions
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	416 (regions without overlapping reads) in a bam/bigWig file
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	417 should be skipped. The default is to treat those
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	418 regions as having a value of zero. The decision to
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	419 skip non-covered regions depends on the interpretation
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	420 of the data. Non-covered regions may represent, for
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	421 example, repetitive regions that should be ignored.
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	422 (default: False)" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	423 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	424
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	425 <xml name="input_save_matrix_values">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	426 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	427 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	428
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	429 <xml name="input_graphic_output_settings">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	430 <conditional name="output" >
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	431 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	432 <option value="no" selected="true">no</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	433 <option value="yes">yes</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	434 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	435 <when value="no" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	436 <when value="yes">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	437 <yield />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	438 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	439 </when>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	440 </conditional>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	441 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	442
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	443
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	444 <xml name="input_image_file_format">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	445 <param argument="--outFileFormat" type="select" label="Image file format">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	446 <option value="png" selected="true">png</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	447 <option value="pdf">pdf</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	448 <option value="svg">svg</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	449 <option value="eps">eps</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	450 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	451 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	452
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	453 <xml name="output_image_file_format">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	454 <data format="png" name="outFileName" label="${tool.name} image">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	455 <change_format>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	456 <when input="output.outFileFormat" value="pdf" format="pdf" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	457 <when input="output.outFileFormat" value="svg" format="svg" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	458 <when input="output.outFileFormat" value="eps" format="eps" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	459 </change_format>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	460 </data>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	461 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	462
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	463 <xml name="output_image_file_format_not_nested">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	464 <data format="png" name="outFileName" label="${tool.name} image">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	465 <change_format>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	466 <when input="outFileFormat" value="pdf" format="pdf" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	467 <when input="outFileFormat" value="svg" format="svg" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	468 <when input="outFileFormat" value="eps" format="eps" />
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	469 </change_format>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	470 </data>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	471 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	472
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	473 <xml name="output_save_matrix_values">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	474 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	475 <filter>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	476 ((
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	477 output['showOutputSettings'] == 'yes' and
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	478 output['saveMatrix'] is True
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	479 ))
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	480 </filter>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	481 </data>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	482 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	483
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	484 <xml name="output_graphic_outputs">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	485 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	486 <filter>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	487 ((
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	488 output['showOutputSettings'] == 'yes' and
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	489 output['saveSortedRegions'] is True
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	490 ))
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	491 </filter>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	492 </data>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	493 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	494
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	495 <xml name="colorMap">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	496 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	497 <option value="RdYlBu" selected="true">RdYlBu</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	498 <option value="Accent">Accent</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	499 <option value="Spectral">Spectral</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	500 <option value="Set1">Set1</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	501 <option value="Set2">Set2</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	502 <option value="Set3">Set3</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	503 <option value="Dark2">Dark2</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	504 <option value="Reds">Reds</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	505 <option value="Oranges">Oranges</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	506 <option value="Greens">Greens</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	507 <option value="Blues">Blues</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	508 <option value="Greys">Greys</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	509 <option value="Purples">Purples</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	510 <option value="Paired">Paired</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	511 <option value="Pastel1">Pastel1</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	512 <option value="Pastel2">Pastel2</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	513 <option value="spring">spring</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	514 <option value="summer">summer</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	515 <option value="autumn">autumn</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	516 <option value="winter">winter</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	517 <option value="hot">hot</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	518 <option value="coolwarm">coolwarm</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	519 <option value="cool">cool</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	520 <option value="seismic">seismic</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	521 <option value="terrain">terrain</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	522 <option value="ocean">ocean</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	523 <option value="rainbow">rainbow</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	524 <option value="bone">bone</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	525 <option value="flag">flag</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	526 <option value="prism">prism</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	527 <option value="cubehelix">cubehelix</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	528 <option value="binary">binary</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	529 <option value="pink">pink</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	530 <option value="gray">gray</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	531 <option value="copper">copper</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	532 <option value="BrBG">BrBG</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	533 <option value="BuGn">BuGn</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	534 <option value="BuPu">BuPu</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	535 <option value="GnBu">GnBu</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	536 <option value="OrRd">OrRd</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	537 <option value="PiYG">PiYG</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	538 <option value="PRGn">PRGn</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	539 <option value="PuOr">PuOr</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	540 <option value="PuRd">PuRd</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	541 <option value="PuBu">PuBu</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	542 <option value="RdBu">RdBu</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	543 <option value="RdGy">RdGy</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	544 <option value="RdPu">RdPu</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	545 <option value="YlGn">YlGn</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	546 <option value="PuBuGn">PuBuGn</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	547 <option value="RdYlGn">RdYlGn</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	548 <option value="YlGnBu">YlGnBu</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	549 <option value="YlOrBr">YlOrBr</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	550 <option value="YlOrRd">YlOrRd</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	551 <option value="gist_gray">gist_gray</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	552 <option value="gist_stern">gist_stern</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	553 <option value="gist_earth">gist_earth</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	554 <option value="gist_yarg">gist_yarg</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	555 <option value="gist_ncar">gist_ncar</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	556 <option value="gist_rainbow">gist_rainbow</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	557 <option value="gist_heat">gist_heat</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	558 <option value="gnuplot">gnuplot</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	559 <option value="gnuplot2">gnuplot2</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	560 <option value="CMRmap">CMRmap</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	561 <option value="bwr">bwr</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	562 <option value="hsv">hsv</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	563 <option value="brg">brg</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	564 <option value="jet">jet</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	565 <option value="afmhot">afmhot</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	566 <option value="Accent_r">Accent reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	567 <option value="Spectral_r">Spectral reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	568 <option value="Set1_r">Set1 reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	569 <option value="Set2_r">Set2 reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	570 <option value="Set3_r">Set3 reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	571 <option value="Dark2_r">Dark2 reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	572 <option value="Reds_r">Reds reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	573 <option value="Oranges_r">Oranges reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	574 <option value="Greens_r">Greens reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	575 <option value="Blues_r">Blues reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	576 <option value="Greys_r">Greys reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	577 <option value="Purples_r">Purples reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	578 <option value="Paired_r">Paired reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	579 <option value="Pastel1_r">Pastel1 reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	580 <option value="Pastel2_r">Pastel2 reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	581 <option value="spring_r">spring reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	582 <option value="summer_r">summer reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	583 <option value="autumn_r">autumn reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	584 <option value="winter_r">winter reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	585 <option value="hot_r">hot reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	586 <option value="coolwarm_r">coolwarm reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	587 <option value="cool_r">cool reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	588 <option value="seismic_r">seismic reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	589 <option value="terrain_r">terrain reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	590 <option value="ocean_r">ocean reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	591 <option value="rainbow_r">rainbow reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	592 <option value="bone_r">bone reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	593 <option value="flag_r">flag reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	594 <option value="prism_r">prism reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	595 <option value="cubehelix_r">cubehelix reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	596 <option value="binary_r">binary reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	597 <option value="pink_r">pink reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	598 <option value="gray_r">gray reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	599 <option value="copper_r">copper reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	600 <option value="BrBG_r">BrBG reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	601 <option value="BuGn_r">BuGn reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	602 <option value="BuPu_r">BuPu reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	603 <option value="GnBu_r">GnBu reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	604 <option value="OrRd_r">OrRd reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	605 <option value="PiYG_r">PiYG reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	606 <option value="PRGn_r">PRGn reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	607 <option value="PuOr_r">PuOr reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	608 <option value="PuRd_r">PuRd reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	609 <option value="PuBu_r">PuBu reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	610 <option value="RdBu_r">RdBu reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	611 <option value="RdGy_r">RdGy reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	612 <option value="RdPu_r">RdPu reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	613 <option value="YlGn_r">YlGn reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	614 <option value="PuBuGn_r">PuBuGn reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	615 <option value="RdYlBu_r">RdYlBu reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	616 <option value="RdYlGn_r">RdYlGn reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	617 <option value="YlGnBu_r">YlGnBu reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	618 <option value="YlOrBr_r">YlOrBr reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	619 <option value="YlOrRd_r">YlOrRd reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	620 <option value="gist_gray_r">gist_gray reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	621 <option value="gist_stern_r">gist_stern reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	622 <option value="gist_earth_r">gist_earth reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	623 <option value="gist_yarg_r">gist_yarg reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	624 <option value="gist_ncar_r">gist_ncar reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	625 <option value="gist_rainbow_r">gist_rainbow reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	626 <option value="gist_heat_r">gist_heat reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	627 <option value="gnuplot_r">gnuplot reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	628 <option value="gnuplot2_r">gnuplot2 reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	629 <option value="CMRmap_r">CMRmap reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	630 <option value="bwr_r">bwr reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	631 <option value="hsv_r">hsv reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	632 <option value="brg_r">brg reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	633 <option value="jet_r">jet reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	634 <option value="afmhot_r">afmhot reversed</option>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	635 </param>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	636
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	637 </xml>
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	638
892146aaf356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: diff changeset	639 </macros>

Mercurial > repos > bgruening > deeptools_bam_coverage

annotate deepTools_macros.xml.orig @ 20:eab93a5553ec draft