deeptools_multi_bigwig_summary: deepTools

annotate deepTools_macros.xml @ 0:bb542efec3b7 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty

author	bgruening
date	Mon, 25 Jan 2016 20:19:55 -0500
parents
children	3da3c3750962

rev	line source
0 bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	1 <macros>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	2
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	3 <xml name="advancedOpt_scaffold">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	4 <conditional name="advancedOpt">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	6 <option value="no" selected="true">no</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	7 <option value="yes">yes</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	8 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	9 <when value="no" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	10 <when value="yes">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	11 <yield/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	12 </when>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	13 </conditional>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	14 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	15
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	20 --extendReads
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	21 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	23 $advancedOpt.centerReads
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	26 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	29 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	32 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	33 </token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	34
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	35 <xml name="heatmap_options">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	36 <expand macro="zMin_zMax" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	37 <expand macro="colorMap" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	38 <expand macro="plotTitle" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	39 <expand macro="plotNumbers" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	40 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	41
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	42 <token name="@HEATMAP_OPTIONS@">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	43 #if str($plotting_type.zMin) != "":
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	44 --zMin $plotting_type.zMin
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	45 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	46 #if str($plotting_type.zMax) != "":
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	47 --zMax $plotting_type.zMax
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	48 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	49 --colorMap '$plotting_type.colorMap'
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	50 $plotting_type.plotNumbers
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	51 --plotTitle '$plotting_type.plotTitle'
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	52 </token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	53
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	54
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	55 <xml name="includeZeros">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	57 label="Include zeros"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty 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." />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	59 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	60
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	61 <xml name="zMin_zMax">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	63 help="If not specified the value is set automatically."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	65 help="If not specified the value is set automatically."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	66 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	67
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	68 <xml name="region_limit_operation">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	69 <param argument="--region" type="text" value=""
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	70 label="Region of the genome to limit the operation to"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty 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"." />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	72 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	73
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	75 <token name="@WRAPPER_VERSION@">2.0.1</token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	76 <xml name="requirements">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	77 <requirements>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	78 <requirement type="package" version="2.7.10">python</requirement>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	79 <requirement type="binary">@BINARY@</requirement>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	80 <requirement type="package" version="2.0.1">deepTools</requirement>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	81 <yield />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	82 </requirements>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	83 <expand macro="stdio" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	84 <version_command>@BINARY@ --version</version_command>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	85 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	86
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	87 <xml name="smoothLength">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	88 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	89 label="Smooth values using the following length (in bases)"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	90 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."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	91 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	92
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	93
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	94 <xml name="kmeans_clustering">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	95 <conditional name="used_multiple_regions">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	96 <param name="used_multiple_regions_options" type="select"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	97 label="Did you compute the matrix with more than one groups of regions?"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	98 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.">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	99 <option value="yes">Yes, I used multiple groups of regions</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	100 <option value="no">No, I used only one group</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	101 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	102 <when value="no">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	103 <conditional name="clustering">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	104 <param name="clustering_options" type="select" label="Clustering algorithm">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	105 <option value="none">No clustering</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	106 <option value="kmeans">Kmeans clustering</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	107 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	108 <when value="kmeans">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	109 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	110 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	111 This only works for data that is not grouped, otherwise only the first group will be clustered.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	112 If more specific clustering methods are required it is advisable to save the underlying matrix and
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	113 run the clustering using other software."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	114 </when>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	115 <when value="none" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	116 </conditional>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	117 </when>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	118 <when value="yes" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	119 </conditional>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	120 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	121
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	122 <token name="@KMEANS_CLUSTERING@">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	123 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	124 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	125 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	126 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	127 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	128 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	129 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	130 </token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	131
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	132 <xml name="samFlags">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	133 <param argument="--samFlagInclude" type="integer" optional="True" value=""
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	134 label="Include reads based on the SAM flag"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	135 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."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	136 <param argument="--samFlagExclude" type="integer" optional="True" value=""
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	137 label="Exclude reads based on the SAM flag"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	138 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."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	139 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	140
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	141 <xml name="read_processing_options">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	142 <expand macro="extendReads" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	143 <expand macro="ignoreDuplicates" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	144 <expand macro="centerReads" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	145 <expand macro="minMappingQuality" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	146 <expand macro="samFlags" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	147 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	148
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	149 <xml name="plotNumbers">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	150 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	151 label="Plot the correlation value"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	152 help="If set, then the correlation number is plotted on top of the heatmap."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	153 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	154
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	155 <xml name="extendReads">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	156 <conditional name="doExtendCustom">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	157 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	158 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.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	159 By default each read mate is extended.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	160 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	161 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	162 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
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	163 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	164 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	165 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	166 <option value="custom">A custom length, which will be applied to ALL reads.</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	167 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	168 <when value="no" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	169 <when value="yes" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	170 <when value="custom">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	171 <param name="extendReadsValue" type="integer" value="300" min="1"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	172 label="Extend reads to the given average fragment size"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	173 help="Extend all reads to this length" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	174 </when>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	175 </conditional>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	176 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	177
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	178 <xml name="corMethod">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	179 <param argument="--corMethod" type="select" label="Correlation method">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	180 <option value="spearman" selected="True">Spearman</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	181 <option value="pearson">Pearson</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	182 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	183 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	184
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	185 <xml name="distanceBetweenBins">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	186 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	187 label="Distance between bins"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	188 help="By default, multiBamSummary considers consecutive bins of
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	189 the specified 'Bin size'. However, to reduce the
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	190 computation time, a larger distance between bins can
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	191 be given. Larger distances result in fewer bins being
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	192 considered."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	193 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	194
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	195 <xml name="centerReads">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	196 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	197 label="Center regions with respect to the fragment length"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	198 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."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	199 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	200
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	201 <xml name="ignoreDuplicates">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	202 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	203 label="Ignore duplicates"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	204 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." />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	205 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	206
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	207 <xml name="sortUsing">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	208 <param argument="--sortUsing" type="select" label="Method used for sorting"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	209 help="For each row the method is computed.">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	210 <option value="mean" selected="true">mean</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	211 <option value="median">median</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	212 <option value="min">min</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	213 <option value="max">max</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	214 <option value="sum">sum</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	215 <option value="region_length">region length</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	216 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	217 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	218
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	219 <xml name="sortRegions">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	220 <param argument="--sortRegions" type="select" label="Sort regions"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	221 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	222 <option value="no">no ordering</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	223 <option value="descend" selected="true">descending order</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	224 <option value="ascend">ascending order</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	225 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	226 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	227
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	228 <xml name="minMappingQuality">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	229 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	230 label="Minimum mapping quality"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	231 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	232 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	233
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	234 <xml name="skipZeros">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	235 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	236 label ="Skip zeros"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	237 help ="If set, then zero counts that happen for all BAM files given are ignored. This may result in fewer considered regions." />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	238 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	239
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	240 <xml name="fragmentLength">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	241 <param argument="--fragmentLength" type="integer" value="300" min="1"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	242 label="Fragment length used for the sequencing"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	243 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."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	244 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	245
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	246 <xml name="scaleFactor">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	247 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	248 help="When used in combination with --normalizeTo1x or
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	249 --normalizeUsingRPKM, the computed scaling factor will
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	250 be multiplied by the given scale factor." />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	251 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	252
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	253 <xml name="scaleFactors">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	254 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	255 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	256 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	257
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	258 <xml name="stdio">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	259 <stdio>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	260 <exit_code range="1:" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	261 <exit_code range=":-1" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	262 <regex match="Error:" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	263 <regex match="Exception:" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	264 <regex match="EXception:" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	265 <regex match="Traceback" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	266 </stdio>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	267 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	268
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	269 <xml name="pseudocount">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	270 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	271 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	272
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	273 <token name="@REFERENCES@">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	274
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	275 .. class:: infomark
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	276
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	277 For more information on the tools, please visit our `help site`_.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	278
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	279 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	280
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	281 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	282
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	283 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	284 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	285 .. _help site: https://deeptools.readthedocs.org/
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	286
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	287 </token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	288 <xml name="citations">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	289 <citations>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	290 <citation type="doi">10.1093/nar/gku365</citation>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	291 <yield />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	292 </citations>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	293 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	294
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	295 <xml name="multiple_input_bams">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	296 <param argument="--bamfiles" type="data" format="bam" min="2"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	297 label="Bam file" multiple="true"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	298 help="The BAM file must be sorted."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	299 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	300
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	301 <xml name="multiple_input_bigwigs">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	302 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	303 label="Bigwig file"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	304 help="A Bigwig file."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	305 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	306
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	307 <xml name="plotTitle">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	308 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	309 label="Title of the plot"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	310 help="Title of the plot, to be printed on top of the generated image." />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	311 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	312
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	313 <token name="@multiple_input_bams@">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	314 <![CDATA[
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	315 #set files=[]
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	316 #set labels=[]
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	317 #for $counter, $bamfile in enumerate($bamfiles):
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	318 ln -s "${bamfile}" "./${counter}.bam" &&
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	319 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	320 #silent $files.append('%s.bam' % $counter)
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	321 #silent $labels.append('%s' % ($bamfile.display_name))
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	322 #end for
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	323 ]]>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	324 </token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	325
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	326 <token name="@multiple_input_bigwigs@">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	327 <![CDATA[
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	328 #set files=[]
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	329 #set labels=[]
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	330 #for $counter, $bigwig in enumerate($bigwigfiles):
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	331 ln -s "${bigwig}" "${counter}.bw" &&
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	332 #silent $files.append('%s.bw' % $counter)
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	333 #silent $labels.append('%s' % ($bigwig.display_name))
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	334 #end for
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	335 ]]>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	336 </token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	337
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	338 <xml name="reference_genome_source">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	339 <conditional name="source">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	340 <param name="ref_source" type="select" label="Reference genome">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	341 <option value="cached">locally cached</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	342 <option value="history">in your history</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	343 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	344 <when value="cached">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	345 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	346 <options from_data_table="lastz_seqs">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	347 <filter type="sort_by" column="1" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	348 <validator type="no_options" message="No indexes are available." />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	349 </options>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	350 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	351 </when>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	352 <when value="history">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	353 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	354 </when>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	355 </conditional>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	356 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	357
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	358 <token name="@reference_genome_source@">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	359 #if $source.ref_source=="history":
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	360 --genome $source.input1
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	361 #else:
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	362 --genome "$source.input1_2bit.fields.path"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	363 #end if
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	364 </token>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	365
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	366 <xml name="effectiveGenomeSize">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	367 <conditional name="effectiveGenomeSize">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	368 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	369 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.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	370 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	371 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.">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	372 <option value="93260000">ce10 (93260000)</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	373 <option value="121400000">dm3 (121400000)</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	374 <option value="2451960000" selected="true">hg19 (2451960000)</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	375 <option value="2150570000">mm9 (2150570000)</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	376 <option value="specific">user specified</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	377 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	378 <when value="specific">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	379 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	380 </when>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	381 <when value="2150570000" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	382 <when value="2451960000" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	383 <when value="121400000" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	384 <when value="93260000" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	385 </conditional>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	386 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	387
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	388 <xml name="skipNAs">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	389 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	390 label="Ignore missing data?"
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	391 help="This parameter determines if non-covered regions
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	392 (regions without overlapping reads) in a bam/bigWig file
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	393 should be skipped. The default is to treat those
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	394 regions as having a value of zero. The decision to
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	395 skip non-covered regions depends on the interpretation
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	396 of the data. Non-covered regions may represent, for
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	397 example, repetitive regions that should be ignored.
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	398 (default: False)" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	399 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	400
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	401 <xml name="input_save_matrix_values">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	402 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	403 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	404
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	405 <xml name="input_graphic_output_settings">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	406 <conditional name="output" >
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	407 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	408 <option value="no" selected="true">no</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	409 <option value="yes">yes</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	410 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	411 <when value="no" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	412 <when value="yes">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	413 <yield />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	414 <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."/>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	415 </when>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	416 </conditional>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	417 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	418
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	419
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	420 <xml name="input_image_file_format">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	421 <param argument="--outFileFormat" type="select" label="Image file format">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	422 <option value="png" selected="true">png</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	423 <option value="pdf">pdf</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	424 <option value="svg">svg</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	425 <option value="eps">eps</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	426 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	427 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	428
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	429 <xml name="output_image_file_format">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	430 <data format="png" name="outFileName" label="${tool.name} image">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	431 <change_format>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	432 <when input="output.outFileFormat" value="pdf" format="pdf" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	433 <when input="output.outFileFormat" value="svg" format="svg" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	434 <when input="output.outFileFormat" value="eps" format="eps" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	435 </change_format>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	436 </data>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	437 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	438
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	439 <xml name="output_image_file_format_not_nested">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	440 <data format="png" name="outFileName" label="${tool.name} image">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	441 <change_format>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	442 <when input="outFileFormat" value="pdf" format="pdf" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	443 <when input="outFileFormat" value="svg" format="svg" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	444 <when input="outFileFormat" value="eps" format="eps" />
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	445 </change_format>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	446 </data>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	447 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	448
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	449 <xml name="output_save_matrix_values">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	450 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	451 <filter>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	452 ((
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	453 output['showOutputSettings'] == 'yes' and
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	454 output['saveMatrix'] is True
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	455 ))
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	456 </filter>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	457 </data>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	458 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	459
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	460 <xml name="output_graphic_outputs">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	461 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	462 <filter>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	463 ((
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	464 output['showOutputSettings'] == 'yes' and
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	465 output['saveSortedRegions'] is True
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	466 ))
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	467 </filter>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	468 </data>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	469 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	470
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	471 <xml name="colorMap">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	472 <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/">
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	473 <option value="RdYlBu" selected="true">RdYlBu</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	474 <option value="Accent">Accent</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	475 <option value="Spectral">Spectral</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	476 <option value="Set1">Set1</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	477 <option value="Set2">Set2</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	478 <option value="Set3">Set3</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	479 <option value="Dark2">Dark2</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	480 <option value="Reds">Reds</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	481 <option value="Oranges">Oranges</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	482 <option value="Greens">Greens</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	483 <option value="Blues">Blues</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	484 <option value="Greys">Greys</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	485 <option value="Purples">Purples</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	486 <option value="Paired">Paired</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	487 <option value="Pastel1">Pastel1</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	488 <option value="Pastel2">Pastel2</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	489 <option value="spring">spring</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	490 <option value="summer">summer</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	491 <option value="autumn">autumn</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	492 <option value="winter">winter</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	493 <option value="hot">hot</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	494 <option value="coolwarm">coolwarm</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	495 <option value="cool">cool</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	496 <option value="seismic">seismic</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	497 <option value="terrain">terrain</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	498 <option value="ocean">ocean</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	499 <option value="rainbow">rainbow</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	500 <option value="bone">bone</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	501 <option value="flag">flag</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	502 <option value="prism">prism</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	503 <option value="cubehelix">cubehelix</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	504 <option value="binary">binary</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	505 <option value="pink">pink</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	506 <option value="gray">gray</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	507 <option value="copper">copper</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	508 <option value="BrBG">BrBG</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	509 <option value="BuGn">BuGn</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	510 <option value="BuPu">BuPu</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	511 <option value="GnBu">GnBu</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	512 <option value="OrRd">OrRd</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	513 <option value="PiYG">PiYG</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	514 <option value="PRGn">PRGn</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	515 <option value="PuOr">PuOr</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	516 <option value="PuRd">PuRd</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	517 <option value="PuBu">PuBu</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	518 <option value="RdBu">RdBu</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	519 <option value="RdGy">RdGy</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	520 <option value="RdPu">RdPu</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	521 <option value="YlGn">YlGn</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	522 <option value="PuBuGn">PuBuGn</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	523 <option value="RdYlGn">RdYlGn</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	524 <option value="YlGnBu">YlGnBu</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	525 <option value="YlOrBr">YlOrBr</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	526 <option value="YlOrRd">YlOrRd</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	527 <option value="gist_gray">gist_gray</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	528 <option value="gist_stern">gist_stern</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	529 <option value="gist_earth">gist_earth</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	530 <option value="gist_yarg">gist_yarg</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	531 <option value="gist_ncar">gist_ncar</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	532 <option value="gist_rainbow">gist_rainbow</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	533 <option value="gist_heat">gist_heat</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	534 <option value="gnuplot">gnuplot</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	535 <option value="gnuplot2">gnuplot2</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	536 <option value="CMRmap">CMRmap</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	537 <option value="bwr">bwr</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	538 <option value="hsv">hsv</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	539 <option value="brg">brg</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	540 <option value="jet">jet</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	541 <option value="afmhot">afmhot</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	542 <option value="Accent_r">Accent reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	543 <option value="Spectral_r">Spectral reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	544 <option value="Set1_r">Set1 reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	545 <option value="Set2_r">Set2 reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	546 <option value="Set3_r">Set3 reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	547 <option value="Dark2_r">Dark2 reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	548 <option value="Reds_r">Reds reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	549 <option value="Oranges_r">Oranges reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	550 <option value="Greens_r">Greens reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	551 <option value="Blues_r">Blues reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	552 <option value="Greys_r">Greys reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	553 <option value="Purples_r">Purples reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	554 <option value="Paired_r">Paired reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	555 <option value="Pastel1_r">Pastel1 reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	556 <option value="Pastel2_r">Pastel2 reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	557 <option value="spring_r">spring reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	558 <option value="summer_r">summer reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	559 <option value="autumn_r">autumn reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	560 <option value="winter_r">winter reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	561 <option value="hot_r">hot reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	562 <option value="coolwarm_r">coolwarm reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	563 <option value="cool_r">cool reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	564 <option value="seismic_r">seismic reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	565 <option value="terrain_r">terrain reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	566 <option value="ocean_r">ocean reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	567 <option value="rainbow_r">rainbow reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	568 <option value="bone_r">bone reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	569 <option value="flag_r">flag reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	570 <option value="prism_r">prism reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	571 <option value="cubehelix_r">cubehelix reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	572 <option value="binary_r">binary reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	573 <option value="pink_r">pink reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	574 <option value="gray_r">gray reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	575 <option value="copper_r">copper reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	576 <option value="BrBG_r">BrBG reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	577 <option value="BuGn_r">BuGn reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	578 <option value="BuPu_r">BuPu reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	579 <option value="GnBu_r">GnBu reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	580 <option value="OrRd_r">OrRd reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	581 <option value="PiYG_r">PiYG reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	582 <option value="PRGn_r">PRGn reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	583 <option value="PuOr_r">PuOr reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	584 <option value="PuRd_r">PuRd reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	585 <option value="PuBu_r">PuBu reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	586 <option value="RdBu_r">RdBu reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	587 <option value="RdGy_r">RdGy reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	588 <option value="RdPu_r">RdPu reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	589 <option value="YlGn_r">YlGn reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	590 <option value="PuBuGn_r">PuBuGn reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	591 <option value="RdYlBu_r">RdYlBu reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	592 <option value="RdYlGn_r">RdYlGn reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	593 <option value="YlGnBu_r">YlGnBu reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	594 <option value="YlOrBr_r">YlOrBr reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	595 <option value="YlOrRd_r">YlOrRd reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	596 <option value="gist_gray_r">gist_gray reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	597 <option value="gist_stern_r">gist_stern reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	598 <option value="gist_earth_r">gist_earth reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	599 <option value="gist_yarg_r">gist_yarg reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	600 <option value="gist_ncar_r">gist_ncar reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	601 <option value="gist_rainbow_r">gist_rainbow reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	602 <option value="gist_heat_r">gist_heat reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	603 <option value="gnuplot_r">gnuplot reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	604 <option value="gnuplot2_r">gnuplot2 reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	605 <option value="CMRmap_r">CMRmap reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	606 <option value="bwr_r">bwr reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	607 <option value="hsv_r">hsv reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	608 <option value="brg_r">brg reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	609 <option value="jet_r">jet reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	610 <option value="afmhot_r">afmhot reversed</option>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	611 </param>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	612
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	613 </xml>
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	614
bb542efec3b7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	615 </macros>

Mercurial > repos > bgruening > deeptools_multi_bigwig_summary

annotate deepTools_macros.xml @ 0:bb542efec3b7 draft