deeptools_multi_bam_summary: deepTools

annotate deepTools_macros.xml.orig @ 13:0f4f3b4ebfa9 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae

author	bgruening
date	Fri, 31 Mar 2017 17:52:40 -0400
parents	f2a582e0314d
children

rev	line source
1 f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	1 <macros>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	2
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	3 <xml name="advancedOpt_scaffold">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	4 <conditional name="advancedOpt">
f2a582e0314d 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" >
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	8 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	9 <when value="no" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	10 <when value="yes">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	11 <yield/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	12 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	13 </conditional>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	14 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	15
f2a582e0314d 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@">
f2a582e0314d 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':
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
f2a582e0314d 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':
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	20 --extendReads
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	21 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	23 $advancedOpt.centerReads
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	26 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	29 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	32 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	33 </token>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	34
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	35 <xml name="heatmap_options">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	36 <expand macro="zMin_zMax" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	37 <expand macro="colorMap" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	38 <expand macro="plotTitle" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	39 <expand macro="plotNumbers" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	40 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	41
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	42 <token name="@HEATMAP_OPTIONS@">
f2a582e0314d 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) != "":
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	44 --zMin $plotting_type.zMin
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	45 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	46 #if str($plotting_type.zMax) != "":
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	47 --zMax $plotting_type.zMax
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	48 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	49 --colorMap '$plotting_type.colorMap'
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	50 $plotting_type.plotNumbers
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	51 --plotTitle '$plotting_type.plotTitle'
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	52 </token>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	53
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	54
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	55 <xml name="includeZeros">
f2a582e0314d 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=""
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	57 label="Include zeros"
f2a582e0314d 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." />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	59 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	60
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	61 <xml name="zMin_zMax">
f2a582e0314d 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"
f2a582e0314d 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."/>
f2a582e0314d 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"
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	66 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	67
f2a582e0314d 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">
f2a582e0314d 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=""
f2a582e0314d 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"
f2a582e0314d 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"." />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	72 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	73
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	75 <<<<<<< HEAD
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	77 =======
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	79 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	80 <xml name="requirements">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	81 <requirements>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	84 <<<<<<< HEAD
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	86 =======
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	88 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	89 <yield />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	90 </requirements>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	91 <expand macro="stdio" />
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	93 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	94
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	95 <xml name="smoothLength">
f2a582e0314d 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"
f2a582e0314d 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)"
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	99 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	100
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	101
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	102 <xml name="kmeans_clustering">
f2a582e0314d 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">
f2a582e0314d 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"
f2a582e0314d 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?"
f2a582e0314d 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.">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	109 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	110 <when value="no">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	111 <conditional name="clustering">
f2a582e0314d 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">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	116 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	117 <when value="kmeans">
f2a582e0314d 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"
f2a582e0314d 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.
f2a582e0314d 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.
f2a582e0314d 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
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	123 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	124 <when value="hclust">
f2a582e0314d 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."
f2a582e0314d 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
f2a582e0314d 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.
f2a582e0314d 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.
f2a582e0314d 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!
f2a582e0314d 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
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	132 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	133 <when value="none" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	134 </conditional>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	135 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	136 <when value="yes" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	137 </conditional>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	138 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	139
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	140 <token name="@KMEANS_CLUSTERING@">
f2a582e0314d 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':
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	142 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	143 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
f2a582e0314d 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
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	145 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	146 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	147 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	148 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
f2a582e0314d 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
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	150 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	151 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	152 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	153 </token>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	154
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	155 <xml name="samFlags">
f2a582e0314d 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=""
f2a582e0314d 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"
f2a582e0314d 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."/>
f2a582e0314d 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=""
f2a582e0314d 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"
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	162 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	163
f2a582e0314d 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">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	165 <expand macro="extendReads" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	166 <expand macro="ignoreDuplicates" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	167 <expand macro="centerReads" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	168 <expand macro="minMappingQuality" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	169 <expand macro="samFlags" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	170 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	171
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	172 <xml name="plotNumbers">
f2a582e0314d 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=""
f2a582e0314d 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"
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	176 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	177
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	178 <xml name="extendReads">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	179 <conditional name="doExtendCustom">
f2a582e0314d 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."
f2a582e0314d 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.
f2a582e0314d 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.
f2a582e0314d 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.
f2a582e0314d 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.
f2a582e0314d 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
f2a582e0314d 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.">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	190 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	191 <when value="no" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	192 <when value="yes" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	193 <when value="custom">
f2a582e0314d 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"
f2a582e0314d 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"
f2a582e0314d 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" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	197 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	198 </conditional>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	199 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	200
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	201 <xml name="corMethod">
f2a582e0314d 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">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	205 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	206 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	207
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	208 <xml name="distanceBetweenBins">
f2a582e0314d 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"
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	210 label="Distance between bins"
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	215 considered."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	216 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	217
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	218 <xml name="centerReads">
f2a582e0314d 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=""
f2a582e0314d 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"
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	222 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	223
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	224 <xml name="ignoreDuplicates">
f2a582e0314d 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=""
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	226 label="Ignore duplicates"
f2a582e0314d 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." />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	228 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	229
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	230 <xml name="sortUsing">
f2a582e0314d 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"
f2a582e0314d 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.">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	239 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	240 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	241
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	242 <xml name="sortRegions">
f2a582e0314d 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"
f2a582e0314d 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.">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	248 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	249 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	250
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	251 <xml name="minMappingQuality">
f2a582e0314d 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"
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	253 label="Minimum mapping quality"
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	255 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	256
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	257 <xml name="skipZeros">
f2a582e0314d 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=""
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	259 label ="Skip zeros"
f2a582e0314d 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." />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	261 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	262
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	263 <xml name="fragmentLength">
f2a582e0314d 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"
f2a582e0314d 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"
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	267 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	268
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	269 <xml name="scaleFactor">
f2a582e0314d 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"
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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." />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	274 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	275
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	276 <xml name="scaleFactors">
f2a582e0314d 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)"/>
f2a582e0314d 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)"/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	279 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	280
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	281 <xml name="stdio">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	282 <stdio>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	283 <exit_code range="1:" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	284 <exit_code range=":-1" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	285 <regex match="Error:" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	286 <regex match="Exception:" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	287 <regex match="EXception:" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	288 <regex match="Traceback" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	289 </stdio>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	290 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	291
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	292 <xml name="pseudocount">
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	294 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	295
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	296 <token name="@REFERENCES@">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	297
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	298 .. class:: infomark
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	299
f2a582e0314d 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`_.
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	301
f2a582e0314d 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
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	303
f2a582e0314d 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`_.
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	305
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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/
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	309
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	310 </token>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	311 <xml name="citations">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	312 <citations>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	314 <yield />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	315 </citations>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	316 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	317
f2a582e0314d 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">
f2a582e0314d 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"
f2a582e0314d 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"
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	322 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	323
f2a582e0314d 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">
f2a582e0314d 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"
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	326 label="Bigwig file"
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	327 help="A Bigwig file."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	328 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	329
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	330 <xml name="plotTitle">
f2a582e0314d 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"
f2a582e0314d 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"
f2a582e0314d 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." />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	334 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	335
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	336
f2a582e0314d 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@">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	338 <![CDATA[
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	339 #set files=[]
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	340 #set labels=[]
f2a582e0314d 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):
f2a582e0314d 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" &&
f2a582e0314d 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" &&
f2a582e0314d 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)
f2a582e0314d 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))
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	346 #end for
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	347 ]]>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	348 </token>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	349
f2a582e0314d 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@">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	351 <![CDATA[
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	352 #set files=[]
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	353 #set labels=[]
f2a582e0314d 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):
f2a582e0314d 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" &&
f2a582e0314d 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)
f2a582e0314d 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))
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	358 #end for
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	359 ]]>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	360 </token>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	361
f2a582e0314d 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">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	363 <conditional name="source">
f2a582e0314d 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">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	367 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	368 <when value="cached">
f2a582e0314d 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">
f2a582e0314d 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">
f2a582e0314d 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" />
f2a582e0314d 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." />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	373 </options>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	374 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	375 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	376 <when value="history">
f2a582e0314d 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" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	378 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	379 </conditional>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	380 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	381
f2a582e0314d 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@">
f2a582e0314d 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":
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	384 --genome $source.input1
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	385 #else:
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	386 --genome "$source.input1_2bit.fields.path"
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	387 #end if
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	388 </token>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	389
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	390 <xml name="effectiveGenomeSize">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	391 <conditional name="effectiveGenomeSize">
f2a582e0314d 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"
f2a582e0314d 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.
f2a582e0314d 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.
f2a582e0314d 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.">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	401 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	402 <when value="specific">
f2a582e0314d 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"/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	404 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	405 <when value="2150570000" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	406 <when value="2451960000" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	407 <when value="121400000" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	408 <when value="93260000" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	409 </conditional>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	410 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	411
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	412 <xml name="skipNAs">
f2a582e0314d 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"
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	414 label="Ignore missing data?"
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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
f2a582e0314d 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.
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	422 (default: False)" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	423 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	424
f2a582e0314d 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">
f2a582e0314d 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"/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	427 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	428
f2a582e0314d 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">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	430 <conditional name="output" >
f2a582e0314d 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" >
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	434 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	435 <when value="no" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	436 <when value="yes">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	437 <yield />
f2a582e0314d 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."/>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	439 </when>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	440 </conditional>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	441 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	442
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	443
f2a582e0314d 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">
f2a582e0314d 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">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	450 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	451 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	452
f2a582e0314d 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">
f2a582e0314d 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">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	455 <change_format>
f2a582e0314d 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" />
f2a582e0314d 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" />
f2a582e0314d 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" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	459 </change_format>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	460 </data>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	461 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	462
f2a582e0314d 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">
f2a582e0314d 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">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	465 <change_format>
f2a582e0314d 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" />
f2a582e0314d 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" />
f2a582e0314d 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" />
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	469 </change_format>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	470 </data>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	471 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	472
f2a582e0314d 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">
f2a582e0314d 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">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	475 <filter>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	476 ((
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	477 output['showOutputSettings'] == 'yes' and
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	478 output['saveMatrix'] is True
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	479 ))
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	480 </filter>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	481 </data>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	482 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	483
f2a582e0314d 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">
f2a582e0314d 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">
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	486 <filter>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	487 ((
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	488 output['showOutputSettings'] == 'yes' and
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	489 output['saveSortedRegions'] is True
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	490 ))
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	491 </filter>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	492 </data>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	493 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	494
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	495 <xml name="colorMap">
f2a582e0314d 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/">
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d 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>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	635 </param>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	636
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	637 </xml>
f2a582e0314d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: diff changeset	638
f2a582e0314d 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_multi_bam_summary

annotate deepTools_macros.xml.orig @ 13:0f4f3b4ebfa9 draft