deeptools_multi_bigwig_summary: deepTools

annotate deepTools_macros.xml @ 5:5cfa07c31ce4 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920

author	bgruening
date	Mon, 15 Feb 2016 10:16:42 -0500
parents	263b4adf3520
children	77276bcad67f

rev	line source
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	1 <macros>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	2
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	3 <xml name="advancedOpt_scaffold">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	4 <conditional name="advancedOpt">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	6 <option value="no" selected="true">no</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	7 <option value="yes">yes</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	8 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	9 <when value="no" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	10 <when value="yes">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	11 <yield/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	12 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	13 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	14 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	15
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	20 --extendReads
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	21 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	23 $advancedOpt.centerReads
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	26 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	29 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	32 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	33 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	34
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	35 <xml name="heatmap_options">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	36 <expand macro="zMin_zMax" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	37 <expand macro="colorMap" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	38 <expand macro="plotTitle" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	39 <expand macro="plotNumbers" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	40 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	41
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	42 <token name="@HEATMAP_OPTIONS@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	43 #if str($plotting_type.zMin) != "":
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	44 --zMin $plotting_type.zMin
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	45 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	46 #if str($plotting_type.zMax) != "":
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	47 --zMax $plotting_type.zMax
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	48 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	49 --colorMap '$plotting_type.colorMap'
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	50 $plotting_type.plotNumbers
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	51 --plotTitle '$plotting_type.plotTitle'
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	52 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	53
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	54
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	55 <xml name="includeZeros">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	57 label="Include zeros"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' 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." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	59 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	60
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	61 <xml name="zMin_zMax">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	63 help="If not specified the value is set automatically."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	65 help="If not specified the value is set automatically."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	66 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	67
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	68 <xml name="region_limit_operation">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	69 <param argument="--region" type="text" value=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	70 label="Region of the genome to limit the operation to"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' 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"." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	72 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	73
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	75 <token name="@WRAPPER_VERSION@">2.1.0</token>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	76 <xml name="requirements">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	77 <requirements>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	78 <requirement type="package" version="2.7.10">python</requirement>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	79 <requirement type="binary">@BINARY@</requirement>
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	80 <requirement type="package" version="2.1.0">deepTools</requirement>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	81 <yield />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	82 </requirements>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	83 <expand macro="stdio" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	84 <version_command>@BINARY@ --version</version_command>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	85 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	86
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	87 <xml name="smoothLength">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	88 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	89 label="Smooth values using the following length (in bases)"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	91 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	92
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	93
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	94 <xml name="kmeans_clustering">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	95 <conditional name="used_multiple_regions">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	96 <param name="used_multiple_regions_options" type="select"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	97 label="Did you compute the matrix with more than one groups of regions?"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' 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.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	99 <option value="yes">Yes, I used multiple groups of regions</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	100 <option value="no">No, I used only one group</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	101 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	102 <when value="no">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	103 <conditional name="clustering">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	104 <param name="clustering_options" type="select" label="Clustering algorithm">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	105 <option value="none">No clustering</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	106 <option value="kmeans">Kmeans clustering</option>
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	107 <option value="hclust">Hierarchical clustering</option>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	108 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	109 <when value="kmeans">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	110 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	111 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	112 This only works for data that is not grouped, otherwise only the first group will be clustered.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	113 If more specific clustering methods are required it is advisable to save the underlying matrix and
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	114 run the clustering using other software."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	115 </when>
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	116 <when value="hclust">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	117 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	118 help="WARNING: This option causes the tool to run for a very long time! When this option is
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	119 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	120 This only works for data that is not grouped, otherwise only the first group will be clustered.
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	121 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	122 If more specific clustering methods are required it is advisable to save the underlying matrix and
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	123 run the clustering using other software."/>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	124 </when>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	125 <when value="none" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	126 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	127 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	128 <when value="yes" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	129 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	130 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	131
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	132 <token name="@KMEANS_CLUSTERING@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	133 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	134 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	135 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	136 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	137 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	138 #end if
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	139 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	140 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	141 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	142 #end if
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	143 #end if
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	144 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	145 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	146
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	147 <xml name="samFlags">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	148 <param argument="--samFlagInclude" type="integer" optional="True" value=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	149 label="Include reads based on the SAM flag"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	150 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	151 <param argument="--samFlagExclude" type="integer" optional="True" value=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	152 label="Exclude reads based on the SAM flag"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	153 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	154 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	155
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	156 <xml name="read_processing_options">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	157 <expand macro="extendReads" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	158 <expand macro="ignoreDuplicates" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	159 <expand macro="centerReads" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	160 <expand macro="minMappingQuality" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	161 <expand macro="samFlags" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	162 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	163
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	164 <xml name="plotNumbers">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	165 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	166 label="Plot the correlation value"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	167 help="If set, then the correlation number is plotted on top of the heatmap."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	168 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	169
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	170 <xml name="extendReads">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	171 <conditional name="doExtendCustom">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	172 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	173 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.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	174 By default each read mate is extended.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	175 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	176 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	177 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
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	178 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	179 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	180 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	181 <option value="custom">A custom length, which will be applied to ALL reads.</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	182 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	183 <when value="no" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	184 <when value="yes" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	185 <when value="custom">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	186 <param name="extendReadsValue" type="integer" value="300" min="1"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	187 label="Extend reads to the given average fragment size"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	188 help="Extend all reads to this length" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	189 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	190 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	191 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	192
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	193 <xml name="corMethod">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	194 <param argument="--corMethod" type="select" label="Correlation method">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	195 <option value="spearman" selected="True">Spearman</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	196 <option value="pearson">Pearson</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	197 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	198 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	199
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	200 <xml name="distanceBetweenBins">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	201 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	202 label="Distance between bins"
2 f297f04e34d3 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: 0 diff changeset	203 help="By default, multiBamSummary considers consecutive bins of
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	204 the specified 'Bin size'. However, to reduce the
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	205 computation time, a larger distance between bins can
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	206 be given. Larger distances result in fewer bins being
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	207 considered."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	208 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	209
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	210 <xml name="centerReads">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	211 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	212 label="Center regions with respect to the fragment length"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	213 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	214 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	215
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	216 <xml name="ignoreDuplicates">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	217 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	218 label="Ignore duplicates"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	219 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." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	220 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	221
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	222 <xml name="sortUsing">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	223 <param argument="--sortUsing" type="select" label="Method used for sorting"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	224 help="For each row the method is computed.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	225 <option value="mean" selected="true">mean</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	226 <option value="median">median</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	227 <option value="min">min</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	228 <option value="max">max</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	229 <option value="sum">sum</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	230 <option value="region_length">region length</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	231 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	232 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	233
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	234 <xml name="sortRegions">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	235 <param argument="--sortRegions" type="select" label="Sort regions"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	236 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	237 <option value="no">no ordering</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	238 <option value="descend" selected="true">descending order</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	239 <option value="ascend">ascending order</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	240 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	241 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	242
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	243 <xml name="minMappingQuality">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	244 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	245 label="Minimum mapping quality"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	246 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	247 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	248
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	249 <xml name="skipZeros">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	250 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	251 label ="Skip zeros"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	252 help ="If set, then zero counts that happen for all BAM files given are ignored. This may result in fewer considered regions." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	253 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	254
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	255 <xml name="fragmentLength">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	256 <param argument="--fragmentLength" type="integer" value="300" min="1"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	257 label="Fragment length used for the sequencing"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	258 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	259 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	260
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	261 <xml name="scaleFactor">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	262 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	263 help="When used in combination with --normalizeTo1x or
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	264 --normalizeUsingRPKM, the computed scaling factor will
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	265 be multiplied by the given scale factor." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	266 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	267
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	268 <xml name="scaleFactors">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	269 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	270 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	271 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	272
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	273 <xml name="stdio">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	274 <stdio>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	275 <exit_code range="1:" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	276 <exit_code range=":-1" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	277 <regex match="Error:" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	278 <regex match="Exception:" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	279 <regex match="EXception:" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	280 <regex match="Traceback" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	281 </stdio>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	282 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	283
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	284 <xml name="pseudocount">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	285 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	286 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	287
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	288 <token name="@REFERENCES@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	289
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	290 .. class:: infomark
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	291
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	292 For more information on the tools, please visit our `help site`_.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	293
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	294 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	295
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	296 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	297
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	298 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	299 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	300 .. _help site: https://deeptools.readthedocs.org/
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	301
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	302 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	303 <xml name="citations">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	304 <citations>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	305 <citation type="doi">10.1093/nar/gku365</citation>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	306 <yield />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	307 </citations>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	308 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	309
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	310 <xml name="multiple_input_bams">
5 5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	311 <param argument="--bamfiles" type="data" format="bam" min="1"
5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	312 label="Bam file" multiple="true"
5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	313 help="The BAM file must be sorted."/>
5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	314 </xml>
5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	315
5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	316 <xml name="multiple_input_bams_min2">
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	317 <param argument="--bamfiles" type="data" format="bam" min="2"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	318 label="Bam file" multiple="true"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	319 help="The BAM file must be sorted."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	320 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	321
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	322 <xml name="multiple_input_bigwigs">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	323 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	324 label="Bigwig file"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	325 help="A Bigwig file."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	326 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	327
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	328 <xml name="plotTitle">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	329 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	330 label="Title of the plot"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	331 help="Title of the plot, to be printed on top of the generated image." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	332 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	333
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	334
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	335 <token name="@multiple_input_bams@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	336 <![CDATA[
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	337 #set files=[]
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	338 #set labels=[]
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	339 #for $counter, $bamfile in enumerate($bamfiles):
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	340 ln -s "${bamfile}" "./${counter}.bam" &&
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	341 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	342 #silent $files.append('%s.bam' % $counter)
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	343 #silent $labels.append('%s' % ($bamfile.display_name))
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	344 #end for
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	345 ]]>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	346 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	347
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	348 <token name="@multiple_input_bigwigs@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	349 <![CDATA[
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	350 #set files=[]
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	351 #set labels=[]
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	352 #for $counter, $bigwig in enumerate($bigwigfiles):
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	353 ln -s "${bigwig}" "${counter}.bw" &&
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	354 #silent $files.append('%s.bw' % $counter)
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	355 #silent $labels.append('%s' % ($bigwig.display_name))
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	356 #end for
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	357 ]]>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	358 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	359
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	360 <xml name="reference_genome_source">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	361 <conditional name="source">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	362 <param name="ref_source" type="select" label="Reference genome">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	363 <option value="cached">locally cached</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	364 <option value="history">in your history</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	365 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	366 <when value="cached">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	367 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	368 <options from_data_table="lastz_seqs">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	369 <filter type="sort_by" column="1" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	370 <validator type="no_options" message="No indexes are available." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	371 </options>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	372 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	373 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	374 <when value="history">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	375 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	376 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	377 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	378 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	379
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	380 <token name="@reference_genome_source@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	381 #if $source.ref_source=="history":
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	382 --genome $source.input1
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	383 #else:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	384 --genome "$source.input1_2bit.fields.path"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	385 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	386 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	387
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	388 <xml name="effectiveGenomeSize">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	389 <conditional name="effectiveGenomeSize">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	390 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	391 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.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	392 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	393 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.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	394 <option value="93260000">ce10 (93260000)</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	395 <option value="121400000">dm3 (121400000)</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	396 <option value="2451960000" selected="true">hg19 (2451960000)</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	397 <option value="2150570000">mm9 (2150570000)</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	398 <option value="specific">user specified</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	399 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	400 <when value="specific">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	401 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	402 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	403 <when value="2150570000" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	404 <when value="2451960000" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	405 <when value="121400000" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	406 <when value="93260000" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	407 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	408 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	409
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	410 <xml name="skipNAs">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	411 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	412 label="Ignore missing data?"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	413 help="This parameter determines if non-covered regions
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	414 (regions without overlapping reads) in a bam/bigWig file
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	415 should be skipped. The default is to treat those
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	416 regions as having a value of zero. The decision to
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	417 skip non-covered regions depends on the interpretation
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	418 of the data. Non-covered regions may represent, for
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	419 example, repetitive regions that should be ignored.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	420 (default: False)" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	421 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	422
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	423 <xml name="input_save_matrix_values">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	424 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	425 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	426
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	427 <xml name="input_graphic_output_settings">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	428 <conditional name="output" >
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	429 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	430 <option value="no" selected="true">no</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	431 <option value="yes">yes</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	432 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	433 <when value="no" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	434 <when value="yes">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	435 <yield />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	436 <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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	437 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	438 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	439 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	440
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	441
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	442 <xml name="input_image_file_format">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	443 <param argument="--outFileFormat" type="select" label="Image file format">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	444 <option value="png" selected="true">png</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	445 <option value="pdf">pdf</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	446 <option value="svg">svg</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	447 <option value="eps">eps</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	448 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	449 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	450
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	451 <xml name="output_image_file_format">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	452 <data format="png" name="outFileName" label="${tool.name} image">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	453 <change_format>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	454 <when input="output.outFileFormat" value="pdf" format="pdf" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	455 <when input="output.outFileFormat" value="svg" format="svg" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	456 <when input="output.outFileFormat" value="eps" format="eps" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	457 </change_format>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	458 </data>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	459 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	460
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	461 <xml name="output_image_file_format_not_nested">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	462 <data format="png" name="outFileName" label="${tool.name} image">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	463 <change_format>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	464 <when input="outFileFormat" value="pdf" format="pdf" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	465 <when input="outFileFormat" value="svg" format="svg" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	466 <when input="outFileFormat" value="eps" format="eps" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	467 </change_format>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	468 </data>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	469 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	470
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	471 <xml name="output_save_matrix_values">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	472 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	473 <filter>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	474 ((
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	475 output['showOutputSettings'] == 'yes' and
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	476 output['saveMatrix'] is True
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	477 ))
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	478 </filter>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	479 </data>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	480 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	481
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	482 <xml name="output_graphic_outputs">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	483 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	484 <filter>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	485 ((
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	486 output['showOutputSettings'] == 'yes' and
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	487 output['saveSortedRegions'] is True
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	488 ))
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	489 </filter>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	490 </data>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	491 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	492
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	493 <xml name="colorMap">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	494 <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/">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	495 <option value="RdYlBu" selected="true">RdYlBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	496 <option value="Accent">Accent</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	497 <option value="Spectral">Spectral</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	498 <option value="Set1">Set1</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	499 <option value="Set2">Set2</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	500 <option value="Set3">Set3</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	501 <option value="Dark2">Dark2</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	502 <option value="Reds">Reds</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	503 <option value="Oranges">Oranges</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	504 <option value="Greens">Greens</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	505 <option value="Blues">Blues</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	506 <option value="Greys">Greys</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	507 <option value="Purples">Purples</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	508 <option value="Paired">Paired</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	509 <option value="Pastel1">Pastel1</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	510 <option value="Pastel2">Pastel2</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	511 <option value="spring">spring</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	512 <option value="summer">summer</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	513 <option value="autumn">autumn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	514 <option value="winter">winter</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	515 <option value="hot">hot</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	516 <option value="coolwarm">coolwarm</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	517 <option value="cool">cool</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	518 <option value="seismic">seismic</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	519 <option value="terrain">terrain</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	520 <option value="ocean">ocean</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	521 <option value="rainbow">rainbow</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	522 <option value="bone">bone</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	523 <option value="flag">flag</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	524 <option value="prism">prism</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	525 <option value="cubehelix">cubehelix</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	526 <option value="binary">binary</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	527 <option value="pink">pink</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	528 <option value="gray">gray</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	529 <option value="copper">copper</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	530 <option value="BrBG">BrBG</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	531 <option value="BuGn">BuGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	532 <option value="BuPu">BuPu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	533 <option value="GnBu">GnBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	534 <option value="OrRd">OrRd</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	535 <option value="PiYG">PiYG</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	536 <option value="PRGn">PRGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	537 <option value="PuOr">PuOr</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	538 <option value="PuRd">PuRd</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	539 <option value="PuBu">PuBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	540 <option value="RdBu">RdBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	541 <option value="RdGy">RdGy</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	542 <option value="RdPu">RdPu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	543 <option value="YlGn">YlGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	544 <option value="PuBuGn">PuBuGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	545 <option value="RdYlGn">RdYlGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	546 <option value="YlGnBu">YlGnBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	547 <option value="YlOrBr">YlOrBr</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	548 <option value="YlOrRd">YlOrRd</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	549 <option value="gist_gray">gist_gray</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	550 <option value="gist_stern">gist_stern</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	551 <option value="gist_earth">gist_earth</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	552 <option value="gist_yarg">gist_yarg</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	553 <option value="gist_ncar">gist_ncar</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	554 <option value="gist_rainbow">gist_rainbow</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	555 <option value="gist_heat">gist_heat</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	556 <option value="gnuplot">gnuplot</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	557 <option value="gnuplot2">gnuplot2</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	558 <option value="CMRmap">CMRmap</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	559 <option value="bwr">bwr</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	560 <option value="hsv">hsv</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	561 <option value="brg">brg</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	562 <option value="jet">jet</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	563 <option value="afmhot">afmhot</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	564 <option value="Accent_r">Accent reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	565 <option value="Spectral_r">Spectral reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	566 <option value="Set1_r">Set1 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	567 <option value="Set2_r">Set2 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	568 <option value="Set3_r">Set3 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	569 <option value="Dark2_r">Dark2 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	570 <option value="Reds_r">Reds reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	571 <option value="Oranges_r">Oranges reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	572 <option value="Greens_r">Greens reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	573 <option value="Blues_r">Blues reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	574 <option value="Greys_r">Greys reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	575 <option value="Purples_r">Purples reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	576 <option value="Paired_r">Paired reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	577 <option value="Pastel1_r">Pastel1 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	578 <option value="Pastel2_r">Pastel2 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	579 <option value="spring_r">spring reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	580 <option value="summer_r">summer reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	581 <option value="autumn_r">autumn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	582 <option value="winter_r">winter reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	583 <option value="hot_r">hot reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	584 <option value="coolwarm_r">coolwarm reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	585 <option value="cool_r">cool reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	586 <option value="seismic_r">seismic reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	587 <option value="terrain_r">terrain reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	588 <option value="ocean_r">ocean reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	589 <option value="rainbow_r">rainbow reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	590 <option value="bone_r">bone reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	591 <option value="flag_r">flag reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	592 <option value="prism_r">prism reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	593 <option value="cubehelix_r">cubehelix reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	594 <option value="binary_r">binary reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	595 <option value="pink_r">pink reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	596 <option value="gray_r">gray reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	597 <option value="copper_r">copper reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	598 <option value="BrBG_r">BrBG reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	599 <option value="BuGn_r">BuGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	600 <option value="BuPu_r">BuPu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	601 <option value="GnBu_r">GnBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	602 <option value="OrRd_r">OrRd reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	603 <option value="PiYG_r">PiYG reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	604 <option value="PRGn_r">PRGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	605 <option value="PuOr_r">PuOr reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	606 <option value="PuRd_r">PuRd reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	607 <option value="PuBu_r">PuBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	608 <option value="RdBu_r">RdBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	609 <option value="RdGy_r">RdGy reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	610 <option value="RdPu_r">RdPu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	611 <option value="YlGn_r">YlGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	612 <option value="PuBuGn_r">PuBuGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	613 <option value="RdYlBu_r">RdYlBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	614 <option value="RdYlGn_r">RdYlGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	615 <option value="YlGnBu_r">YlGnBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	616 <option value="YlOrBr_r">YlOrBr reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	617 <option value="YlOrRd_r">YlOrRd reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	618 <option value="gist_gray_r">gist_gray reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	619 <option value="gist_stern_r">gist_stern reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	620 <option value="gist_earth_r">gist_earth reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	621 <option value="gist_yarg_r">gist_yarg reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	622 <option value="gist_ncar_r">gist_ncar reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	623 <option value="gist_rainbow_r">gist_rainbow reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	624 <option value="gist_heat_r">gist_heat reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	625 <option value="gnuplot_r">gnuplot reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	626 <option value="gnuplot2_r">gnuplot2 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	627 <option value="CMRmap_r">CMRmap reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	628 <option value="bwr_r">bwr reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	629 <option value="hsv_r">hsv reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	630 <option value="brg_r">brg reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	631 <option value="jet_r">jet reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	632 <option value="afmhot_r">afmhot reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	633 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	634
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	635 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	636
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	637 </macros>

Mercurial > repos > bgruening > deeptools_multi_bigwig_summary

annotate deepTools_macros.xml @ 5:5cfa07c31ce4 draft