deeptools_bam_compare: deepTools_macros.xml.orig annotate

annotate deepTools_macros.xml.orig @ 4:732726f3f986 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c-dirty

author	bgruening
date	Thu, 10 Mar 2016 03:25:09 -0500
parents	e237a134059a
children

rev	line source
1 e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	1 <macros>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	2
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	3 <xml name="advancedOpt_scaffold">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	4 <conditional name="advancedOpt">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	6 <option value="no" selected="true">no</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	7 <option value="yes">yes</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	8 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	9 <when value="no" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	10 <when value="yes">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	11 <yield/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	12 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	13 </conditional>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	14 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	15
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	20 --extendReads
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	21 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	23 $advancedOpt.centerReads
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	26 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	29 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	32 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	33 </token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	34
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	35 <xml name="heatmap_options">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	36 <expand macro="zMin_zMax" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	37 <expand macro="colorMap" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	38 <expand macro="plotTitle" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	39 <expand macro="plotNumbers" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	40 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	41
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	42 <token name="@HEATMAP_OPTIONS@">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	43 #if str($plotting_type.zMin) != "":
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	44 --zMin $plotting_type.zMin
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	45 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	46 #if str($plotting_type.zMax) != "":
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	47 --zMax $plotting_type.zMax
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	48 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	49 --colorMap '$plotting_type.colorMap'
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	50 $plotting_type.plotNumbers
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	51 --plotTitle '$plotting_type.plotTitle'
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	52 </token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	53
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	54
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	55 <xml name="includeZeros">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	57 label="Include zeros"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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." />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	59 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	60
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	61 <xml name="zMin_zMax">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	63 help="If not specified the value is set automatically."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	65 help="If not specified the value is set automatically."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	66 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	67
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	68 <xml name="region_limit_operation">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	69 <param argument="--region" type="text" value=""
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	70 label="Region of the genome to limit the operation to"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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"." />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	72 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	73
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	75 <<<<<<< HEAD
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	76 <token name="@WRAPPER_VERSION@">2.0.1.0</token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	77 =======
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	78 <token name="@WRAPPER_VERSION@">2.1.0</token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	79 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	80 <xml name="requirements">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	81 <requirements>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	82 <requirement type="package" version="2.7.10">python</requirement>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	83 <requirement type="binary">@BINARY@</requirement>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	84 <<<<<<< HEAD
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	85 <requirement type="package" version="2.0.1">deepTools</requirement>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	86 =======
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	87 <requirement type="package" version="2.1.0">deepTools</requirement>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	88 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	89 <yield />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	90 </requirements>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	91 <expand macro="stdio" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	92 <version_command>@BINARY@ --version</version_command>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	93 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	94
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	95 <xml name="smoothLength">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	96 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	97 label="Smooth values using the following length (in bases)"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	99 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	100
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	101
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	102 <xml name="kmeans_clustering">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	103 <conditional name="used_multiple_regions">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	104 <param name="used_multiple_regions_options" type="select"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	105 label="Did you compute the matrix with more than one groups of regions?"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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.">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	107 <option value="yes">Yes, I used multiple groups of regions</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	108 <option value="no">No, I used only one group</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	109 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	110 <when value="no">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	111 <conditional name="clustering">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	112 <param name="clustering_options" type="select" label="Clustering algorithm">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	113 <option value="none">No clustering</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	114 <option value="kmeans">Kmeans clustering</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	115 <option value="hclust">Hierarchical clustering</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	116 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	117 <when value="kmeans">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	118 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	119 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	120 This only works for data that is not grouped, otherwise only the first group will be clustered.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	121 If more specific clustering methods are required it is advisable to save the underlying matrix and
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	122 run the clustering using other software."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	123 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	124 <when value="hclust">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	125 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	126 help="WARNING: This option causes the tool to run for a very long time! When this option is
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	127 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	128 This only works for data that is not grouped, otherwise only the first group will be clustered.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	129 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	130 If more specific clustering methods are required it is advisable to save the underlying matrix and
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	131 run the clustering using other software."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	132 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	133 <when value="none" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	134 </conditional>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	135 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	136 <when value="yes" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	137 </conditional>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	138 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	139
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	140 <token name="@KMEANS_CLUSTERING@">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	141 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	142 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	143 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	144 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	145 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	146 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	147 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	148 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	149 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	150 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	151 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	152 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	153 </token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	154
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	155 <xml name="samFlags">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	156 <param argument="--samFlagInclude" type="integer" optional="True" value=""
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	157 label="Include reads based on the SAM flag"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	159 <param argument="--samFlagExclude" type="integer" optional="True" value=""
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	160 label="Exclude reads based on the SAM flag"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	162 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	163
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	164 <xml name="read_processing_options">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	165 <expand macro="extendReads" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	166 <expand macro="ignoreDuplicates" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	167 <expand macro="centerReads" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	168 <expand macro="minMappingQuality" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	169 <expand macro="samFlags" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	170 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	171
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	172 <xml name="plotNumbers">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	173 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	174 label="Plot the correlation value"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	175 help="If set, then the correlation number is plotted on top of the heatmap."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	176 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	177
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	178 <xml name="extendReads">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	179 <conditional name="doExtendCustom">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	180 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	182 By default each read mate is extended.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	184 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	186 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	187 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	188 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	189 <option value="custom">A custom length, which will be applied to ALL reads.</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	190 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	191 <when value="no" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	192 <when value="yes" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	193 <when value="custom">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	194 <param name="extendReadsValue" type="integer" value="300" min="1"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	195 label="Extend reads to the given average fragment size"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	196 help="Extend all reads to this length" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	197 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	198 </conditional>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	199 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	200
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	201 <xml name="corMethod">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	202 <param argument="--corMethod" type="select" label="Correlation method">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	203 <option value="spearman" selected="True">Spearman</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	204 <option value="pearson">Pearson</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	205 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	206 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	207
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	208 <xml name="distanceBetweenBins">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	209 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	210 label="Distance between bins"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	211 help="By default, multiBamSummary considers consecutive bins of
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	212 the specified 'Bin size'. However, to reduce the
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	213 computation time, a larger distance between bins can
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	214 be given. Larger distances result in fewer bins being
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	215 considered."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	216 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	217
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	218 <xml name="centerReads">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	219 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	220 label="Center regions with respect to the fragment length"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	222 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	223
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	224 <xml name="ignoreDuplicates">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	225 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	226 label="Ignore duplicates"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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." />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	228 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	229
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	230 <xml name="sortUsing">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	231 <param argument="--sortUsing" type="select" label="Method used for sorting"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	232 help="For each row the method is computed.">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	233 <option value="mean" selected="true">mean</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	234 <option value="median">median</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	235 <option value="min">min</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	236 <option value="max">max</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	237 <option value="sum">sum</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	238 <option value="region_length">region length</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	239 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	240 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	241
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	242 <xml name="sortRegions">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	243 <param argument="--sortRegions" type="select" label="Sort regions"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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.">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	245 <option value="no">no ordering</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	246 <option value="descend" selected="true">descending order</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	247 <option value="ascend">ascending order</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	248 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	249 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	250
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	251 <xml name="minMappingQuality">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	252 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	253 label="Minimum mapping quality"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	254 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	255 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	256
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	257 <xml name="skipZeros">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	258 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	259 label ="Skip zeros"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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." />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	261 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	262
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	263 <xml name="fragmentLength">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	264 <param argument="--fragmentLength" type="integer" value="300" min="1"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	265 label="Fragment length used for the sequencing"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	267 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	268
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	269 <xml name="scaleFactor">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	270 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	271 help="When used in combination with --normalizeTo1x or
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	272 --normalizeUsingRPKM, the computed scaling factor will
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	273 be multiplied by the given scale factor." />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	274 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	275
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	276 <xml name="scaleFactors">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	277 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	278 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	279 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	280
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	281 <xml name="stdio">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	282 <stdio>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	283 <exit_code range="1:" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	284 <exit_code range=":-1" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	285 <regex match="Error:" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	286 <regex match="Exception:" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	287 <regex match="EXception:" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	288 <regex match="Traceback" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	289 </stdio>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	290 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	291
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	292 <xml name="pseudocount">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	293 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	294 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	295
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	296 <token name="@REFERENCES@">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	297
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	298 .. class:: infomark
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	299
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	300 For more information on the tools, please visit our `help site`_.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	301
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	303
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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`_.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	305
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	306 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	307 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	308 .. _help site: https://deeptools.readthedocs.org/
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	309
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	310 </token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	311 <xml name="citations">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	312 <citations>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	313 <citation type="doi">10.1093/nar/gku365</citation>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	314 <yield />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	315 </citations>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	316 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	317
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	318 <xml name="multiple_input_bams">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	319 <param argument="--bamfiles" type="data" format="bam" min="2"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	320 label="Bam file" multiple="true"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	321 help="The BAM file must be sorted."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	322 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	323
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	324 <xml name="multiple_input_bigwigs">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	325 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	326 label="Bigwig file"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	327 help="A Bigwig file."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	328 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	329
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	330 <xml name="plotTitle">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	331 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	332 label="Title of the plot"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	333 help="Title of the plot, to be printed on top of the generated image." />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	334 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	335
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	336
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	337 <token name="@multiple_input_bams@">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	338 <![CDATA[
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	339 #set files=[]
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	340 #set labels=[]
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	341 #for $counter, $bamfile in enumerate($bamfiles):
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	342 ln -s "${bamfile}" "./${counter}.bam" &&
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	343 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	344 #silent $files.append('%s.bam' % $counter)
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	345 #silent $labels.append('%s' % ($bamfile.display_name))
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	346 #end for
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	347 ]]>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	348 </token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	349
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	350 <token name="@multiple_input_bigwigs@">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	351 <![CDATA[
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	352 #set files=[]
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	353 #set labels=[]
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	354 #for $counter, $bigwig in enumerate($bigwigfiles):
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	355 ln -s "${bigwig}" "${counter}.bw" &&
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	356 #silent $files.append('%s.bw' % $counter)
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	357 #silent $labels.append('%s' % ($bigwig.display_name))
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	358 #end for
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	359 ]]>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	360 </token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	361
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	362 <xml name="reference_genome_source">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	363 <conditional name="source">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	364 <param name="ref_source" type="select" label="Reference genome">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	365 <option value="cached">locally cached</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	366 <option value="history">in your history</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	367 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	368 <when value="cached">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	370 <options from_data_table="lastz_seqs">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	371 <filter type="sort_by" column="1" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	372 <validator type="no_options" message="No indexes are available." />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	373 </options>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	374 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	375 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	376 <when value="history">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	377 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	378 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	379 </conditional>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	380 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	381
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	382 <token name="@reference_genome_source@">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	383 #if $source.ref_source=="history":
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	384 --genome $source.input1
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	385 #else:
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	386 --genome "$source.input1_2bit.fields.path"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	387 #end if
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	388 </token>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	389
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	390 <xml name="effectiveGenomeSize">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	391 <conditional name="effectiveGenomeSize">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	392 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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.">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	396 <option value="93260000">ce10 (93260000)</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	397 <option value="121400000">dm3 (121400000)</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	398 <option value="2451960000" selected="true">hg19 (2451960000)</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	399 <option value="2150570000">mm9 (2150570000)</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	400 <option value="specific">user specified</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	401 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	402 <when value="specific">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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"/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	404 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	405 <when value="2150570000" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	406 <when value="2451960000" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	407 <when value="121400000" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	408 <when value="93260000" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	409 </conditional>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	410 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	411
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	412 <xml name="skipNAs">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	413 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	414 label="Ignore missing data?"
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	415 help="This parameter determines if non-covered regions
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	416 (regions without overlapping reads) in a bam/bigWig file
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	417 should be skipped. The default is to treat those
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	418 regions as having a value of zero. The decision to
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	419 skip non-covered regions depends on the interpretation
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	420 of the data. Non-covered regions may represent, for
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	421 example, repetitive regions that should be ignored.
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	422 (default: False)" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	423 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	424
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	425 <xml name="input_save_matrix_values">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	426 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	427 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	428
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	429 <xml name="input_graphic_output_settings">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	430 <conditional name="output" >
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	431 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	432 <option value="no" selected="true">no</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	433 <option value="yes">yes</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	434 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	435 <when value="no" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	436 <when value="yes">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	437 <yield />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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."/>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	439 </when>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	440 </conditional>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	441 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	442
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	443
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	444 <xml name="input_image_file_format">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	445 <param argument="--outFileFormat" type="select" label="Image file format">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	446 <option value="png" selected="true">png</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	447 <option value="pdf">pdf</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	448 <option value="svg">svg</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	449 <option value="eps">eps</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	450 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	451 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	452
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	453 <xml name="output_image_file_format">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	454 <data format="png" name="outFileName" label="${tool.name} image">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	455 <change_format>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	456 <when input="output.outFileFormat" value="pdf" format="pdf" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	457 <when input="output.outFileFormat" value="svg" format="svg" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	458 <when input="output.outFileFormat" value="eps" format="eps" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	459 </change_format>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	460 </data>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	461 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	462
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	463 <xml name="output_image_file_format_not_nested">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	464 <data format="png" name="outFileName" label="${tool.name} image">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	465 <change_format>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	466 <when input="outFileFormat" value="pdf" format="pdf" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	467 <when input="outFileFormat" value="svg" format="svg" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	468 <when input="outFileFormat" value="eps" format="eps" />
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	469 </change_format>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	470 </data>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	471 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	472
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	473 <xml name="output_save_matrix_values">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	474 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	475 <filter>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	476 ((
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	477 output['showOutputSettings'] == 'yes' and
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	478 output['saveMatrix'] is True
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	479 ))
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	480 </filter>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	481 </data>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	482 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	483
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	484 <xml name="output_graphic_outputs">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	485 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	486 <filter>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	487 ((
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	488 output['showOutputSettings'] == 'yes' and
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	489 output['saveSortedRegions'] is True
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	490 ))
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	491 </filter>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	492 </data>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	493 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	494
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	495 <xml name="colorMap">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 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/">
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	497 <option value="RdYlBu" selected="true">RdYlBu</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	498 <option value="Accent">Accent</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	499 <option value="Spectral">Spectral</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	500 <option value="Set1">Set1</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	501 <option value="Set2">Set2</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	502 <option value="Set3">Set3</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	503 <option value="Dark2">Dark2</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	504 <option value="Reds">Reds</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	505 <option value="Oranges">Oranges</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	506 <option value="Greens">Greens</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	507 <option value="Blues">Blues</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	508 <option value="Greys">Greys</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	509 <option value="Purples">Purples</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	510 <option value="Paired">Paired</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	511 <option value="Pastel1">Pastel1</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	512 <option value="Pastel2">Pastel2</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	513 <option value="spring">spring</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	514 <option value="summer">summer</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	515 <option value="autumn">autumn</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	516 <option value="winter">winter</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	517 <option value="hot">hot</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	518 <option value="coolwarm">coolwarm</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	519 <option value="cool">cool</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	520 <option value="seismic">seismic</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	521 <option value="terrain">terrain</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	522 <option value="ocean">ocean</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	523 <option value="rainbow">rainbow</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	524 <option value="bone">bone</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	525 <option value="flag">flag</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	526 <option value="prism">prism</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	527 <option value="cubehelix">cubehelix</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	528 <option value="binary">binary</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	529 <option value="pink">pink</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	530 <option value="gray">gray</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	531 <option value="copper">copper</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	532 <option value="BrBG">BrBG</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	533 <option value="BuGn">BuGn</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	534 <option value="BuPu">BuPu</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	535 <option value="GnBu">GnBu</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	536 <option value="OrRd">OrRd</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	537 <option value="PiYG">PiYG</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	538 <option value="PRGn">PRGn</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	539 <option value="PuOr">PuOr</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	540 <option value="PuRd">PuRd</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	541 <option value="PuBu">PuBu</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	542 <option value="RdBu">RdBu</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	543 <option value="RdGy">RdGy</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	544 <option value="RdPu">RdPu</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	545 <option value="YlGn">YlGn</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	546 <option value="PuBuGn">PuBuGn</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	547 <option value="RdYlGn">RdYlGn</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	548 <option value="YlGnBu">YlGnBu</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	549 <option value="YlOrBr">YlOrBr</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	550 <option value="YlOrRd">YlOrRd</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	551 <option value="gist_gray">gist_gray</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	552 <option value="gist_stern">gist_stern</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	553 <option value="gist_earth">gist_earth</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	554 <option value="gist_yarg">gist_yarg</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	555 <option value="gist_ncar">gist_ncar</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	556 <option value="gist_rainbow">gist_rainbow</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	557 <option value="gist_heat">gist_heat</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	558 <option value="gnuplot">gnuplot</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	559 <option value="gnuplot2">gnuplot2</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	560 <option value="CMRmap">CMRmap</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	561 <option value="bwr">bwr</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	562 <option value="hsv">hsv</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	563 <option value="brg">brg</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	564 <option value="jet">jet</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	565 <option value="afmhot">afmhot</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	566 <option value="Accent_r">Accent reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	567 <option value="Spectral_r">Spectral reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	568 <option value="Set1_r">Set1 reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	569 <option value="Set2_r">Set2 reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	570 <option value="Set3_r">Set3 reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	571 <option value="Dark2_r">Dark2 reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	572 <option value="Reds_r">Reds reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	573 <option value="Oranges_r">Oranges reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	574 <option value="Greens_r">Greens reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	575 <option value="Blues_r">Blues reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	576 <option value="Greys_r">Greys reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	577 <option value="Purples_r">Purples reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	578 <option value="Paired_r">Paired reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	579 <option value="Pastel1_r">Pastel1 reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	580 <option value="Pastel2_r">Pastel2 reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	581 <option value="spring_r">spring reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	582 <option value="summer_r">summer reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	583 <option value="autumn_r">autumn reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	584 <option value="winter_r">winter reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	585 <option value="hot_r">hot reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	586 <option value="coolwarm_r">coolwarm reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	587 <option value="cool_r">cool reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	588 <option value="seismic_r">seismic reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	589 <option value="terrain_r">terrain reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	590 <option value="ocean_r">ocean reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	591 <option value="rainbow_r">rainbow reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	592 <option value="bone_r">bone reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	593 <option value="flag_r">flag reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	594 <option value="prism_r">prism reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	595 <option value="cubehelix_r">cubehelix reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	596 <option value="binary_r">binary reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	597 <option value="pink_r">pink reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	598 <option value="gray_r">gray reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	599 <option value="copper_r">copper reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	600 <option value="BrBG_r">BrBG reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	601 <option value="BuGn_r">BuGn reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	602 <option value="BuPu_r">BuPu reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	603 <option value="GnBu_r">GnBu reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	604 <option value="OrRd_r">OrRd reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	605 <option value="PiYG_r">PiYG reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	606 <option value="PRGn_r">PRGn reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	607 <option value="PuOr_r">PuOr reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	608 <option value="PuRd_r">PuRd reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	609 <option value="PuBu_r">PuBu reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	610 <option value="RdBu_r">RdBu reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	611 <option value="RdGy_r">RdGy reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	612 <option value="RdPu_r">RdPu reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	613 <option value="YlGn_r">YlGn reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	614 <option value="PuBuGn_r">PuBuGn reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	615 <option value="RdYlBu_r">RdYlBu reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	616 <option value="RdYlGn_r">RdYlGn reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	617 <option value="YlGnBu_r">YlGnBu reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	618 <option value="YlOrBr_r">YlOrBr reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	619 <option value="YlOrRd_r">YlOrRd reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	620 <option value="gist_gray_r">gist_gray reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	621 <option value="gist_stern_r">gist_stern reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	622 <option value="gist_earth_r">gist_earth reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	623 <option value="gist_yarg_r">gist_yarg reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	624 <option value="gist_ncar_r">gist_ncar reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	625 <option value="gist_rainbow_r">gist_rainbow reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	626 <option value="gist_heat_r">gist_heat reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	627 <option value="gnuplot_r">gnuplot reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	628 <option value="gnuplot2_r">gnuplot2 reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	629 <option value="CMRmap_r">CMRmap reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	630 <option value="bwr_r">bwr reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	631 <option value="hsv_r">hsv reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	632 <option value="brg_r">brg reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	633 <option value="jet_r">jet reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	634 <option value="afmhot_r">afmhot reversed</option>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	635 </param>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	636
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	637 </xml>
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	638
e237a134059a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	639 </macros>

Mercurial > repos > bgruening > deeptools_bam_compare

annotate deepTools_macros.xml.orig @ 4:732726f3f986 draft