deeptools_plot_fingerprint: deepTools

annotate deepTools_macros.xml @ 10:d0a10af43611 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty

author	bgruening
date	Sun, 24 Apr 2016 14:04:57 -0400
parents	9a16cdd40ef6
children	eb393451c67c

rev	line source
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	1 <macros>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	2
bb874a0121d5 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">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	4 <conditional name="advancedOpt">
bb874a0121d5 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" >
bb874a0121d5 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>
bb874a0121d5 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>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	8 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	9 <when value="no" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	10 <when value="yes">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	11 <yield/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	12 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	13 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	14 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	15
bb874a0121d5 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@">
bb874a0121d5 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':
bb874a0121d5 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
bb874a0121d5 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':
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	20 --extendReads
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	21 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	23 $advancedOpt.centerReads
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	26 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	29 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	32 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	33 </token>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	34
bb874a0121d5 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">
bb874a0121d5 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" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	37 <expand macro="colorMap" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	38 <expand macro="plotTitle" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	39 <expand macro="plotNumbers" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	40 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	41
bb874a0121d5 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@">
bb874a0121d5 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) != "":
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	44 --zMin $plotting_type.zMin
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	45 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	46 #if str($plotting_type.zMax) != "":
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	47 --zMax $plotting_type.zMax
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	48 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	49 --colorMap '$plotting_type.colorMap'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	50 $plotting_type.plotNumbers
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	51 --plotTitle '$plotting_type.plotTitle'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	52 </token>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	53
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	54
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	55 <xml name="includeZeros">
bb874a0121d5 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=""
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	57 label="Include zeros"
bb874a0121d5 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." />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	59 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	60
bb874a0121d5 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">
bb874a0121d5 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"
bb874a0121d5 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."/>
bb874a0121d5 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"
bb874a0121d5 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."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	66 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	67
bb874a0121d5 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">
bb874a0121d5 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=""
bb874a0121d5 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"
10 d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 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".">
d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	72 <sanitizer>
d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	73 <valid initial="string.letters,string.digits">
d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	74 <add value="\|"/>
d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	75 </valid>
d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	76 </sanitizer>
d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	77 </param>
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	78 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	79
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	80 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
10 d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	81 <token name="@WRAPPER_VERSION@">2.2.3</token>
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	82 <xml name="requirements">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	83 <requirements>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	84 <requirement type="package" version="2.7.10">python</requirement>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	85 <requirement type="binary">@BINARY@</requirement>
10 d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	86 <requirement type="package" version="2.2.3">deepTools</requirement>
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	87 <yield />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	88 </requirements>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	89 <expand macro="stdio" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	90 <version_command>@BINARY@ --version</version_command>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	91 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	92
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	93 <xml name="smoothLength">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	94 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	95 label="Smooth values using the following length (in bases)"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	96 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."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	97 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	98
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	99
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	100 <xml name="kmeans_clustering">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	101 <conditional name="used_multiple_regions">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	102 <param name="used_multiple_regions_options" type="select"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	103 label="Did you compute the matrix with more than one groups of regions?"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	104 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.">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	105 <option value="yes">Yes, I used multiple groups of regions</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	106 <option value="no">No, I used only one group</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	107 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	108 <when value="no">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	109 <conditional name="clustering">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	110 <param name="clustering_options" type="select" label="Clustering algorithm">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	111 <option value="none">No clustering</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	112 <option value="kmeans">Kmeans clustering</option>
4 30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	113 <option value="hclust">Hierarchical clustering</option>
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	114 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	115 <when value="kmeans">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	116 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	117 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	118 This only works for data that is not grouped, otherwise only the first group will be clustered.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	119 If more specific clustering methods are required it is advisable to save the underlying matrix and
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	120 run the clustering using other software."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	121 </when>
4 30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	122 <when value="hclust">
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	123 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	124 help="WARNING: This option causes the tool to run for a very long time! When this option is
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	125 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	126 This only works for data that is not grouped, otherwise only the first group will be clustered.
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	127 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	128 If more specific clustering methods are required it is advisable to save the underlying matrix and
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	129 run the clustering using other software."/>
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	130 </when>
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	131 <when value="none" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	132 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	133 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	134 <when value="yes" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	135 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	136 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	137
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	138 <token name="@KMEANS_CLUSTERING@">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	139 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	140 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	141 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	142 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	143 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	144 #end if
4 30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	145 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	146 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	147 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	148 #end if
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	149 #end if
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	150 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	151 </token>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	152
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	153 <xml name="samFlags">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	154 <param argument="--samFlagInclude" type="integer" optional="True" value=""
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	155 label="Include reads based on the SAM flag"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	156 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."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	157 <param argument="--samFlagExclude" type="integer" optional="True" value=""
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	158 label="Exclude reads based on the SAM flag"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	159 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."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	160 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	161
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	162 <xml name="read_processing_options">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	163 <expand macro="extendReads" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	164 <expand macro="ignoreDuplicates" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	165 <expand macro="centerReads" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	166 <expand macro="minMappingQuality" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	167 <expand macro="samFlags" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	168 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	169
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	170 <xml name="plotNumbers">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	171 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	172 label="Plot the correlation value"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	173 help="If set, then the correlation number is plotted on top of the heatmap."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	174 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	175
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	176 <xml name="extendReads">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	177 <conditional name="doExtendCustom">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	178 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	179 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.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	180 By default each read mate is extended.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	181 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	182 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	183 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
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	184 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	185 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	186 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	187 <option value="custom">A custom length, which will be applied to ALL reads.</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	188 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	189 <when value="no" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	190 <when value="yes" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	191 <when value="custom">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	192 <param name="extendReadsValue" type="integer" value="300" min="1"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	193 label="Extend reads to the given average fragment size"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	194 help="Extend all reads to this length" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	195 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	196 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	197 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	198
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	199 <xml name="corMethod">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	200 <param argument="--corMethod" type="select" label="Correlation method">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	201 <option value="spearman" selected="True">Spearman</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	202 <option value="pearson">Pearson</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	203 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	204 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	205
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	206 <xml name="distanceBetweenBins">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	207 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	208 label="Distance between bins"
2 06704d286748 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: 0 diff changeset	209 help="By default, multiBamSummary considers consecutive bins of
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	210 the specified 'Bin size'. However, to reduce the
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	211 computation time, a larger distance between bins can
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	212 be given. Larger distances result in fewer bins being
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	213 considered."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	214 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	215
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	216 <xml name="centerReads">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	217 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	218 label="Center regions with respect to the fragment length"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	219 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."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	220 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	221
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	222 <xml name="ignoreDuplicates">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	223 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	224 label="Ignore duplicates"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	225 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." />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	226 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	227
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	228 <xml name="sortUsing">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	229 <param argument="--sortUsing" type="select" label="Method used for sorting"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	230 help="For each row the method is computed.">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	231 <option value="mean" selected="true">mean</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	232 <option value="median">median</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	233 <option value="min">min</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	234 <option value="max">max</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	235 <option value="sum">sum</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	236 <option value="region_length">region length</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	237 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	238 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	239
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	240 <xml name="sortRegions">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	241 <param argument="--sortRegions" type="select" label="Sort regions"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	242 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	243 <option value="no">no ordering</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	244 <option value="descend" selected="true">descending order</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	245 <option value="ascend">ascending order</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	246 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	247 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	248
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	249 <xml name="minMappingQuality">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	250 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	251 label="Minimum mapping quality"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	252 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	253 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	254
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	255 <xml name="skipZeros">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	256 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	257 label ="Skip zeros"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	258 help ="If set, then zero counts that happen for all BAM files given are ignored. This may result in fewer considered regions." />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	259 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	260
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	261 <xml name="fragmentLength">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	262 <param argument="--fragmentLength" type="integer" value="300" min="1"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	263 label="Fragment length used for the sequencing"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	264 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."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	265 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	266
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	267 <xml name="scaleFactor">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	268 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	269 help="When used in combination with --normalizeTo1x or
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	270 --normalizeUsingRPKM, the computed scaling factor will
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	271 be multiplied by the given scale factor." />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	272 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	273
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	274 <xml name="scaleFactors">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	275 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	276 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	277 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	278
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	279 <xml name="stdio">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	280 <stdio>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	281 <exit_code range="1:" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	282 <exit_code range=":-1" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	283 <regex match="Error:" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	284 <regex match="Exception:" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	285 <regex match="EXception:" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	286 <regex match="Traceback" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	287 </stdio>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	288 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	289
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	290 <xml name="pseudocount">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	291 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	292 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	293
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	294 <token name="@REFERENCES@">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	295
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	296 .. class:: infomark
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	297
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	298 For more information on the tools, please visit our `help site`_.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	299
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	300 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	301
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	302 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	303
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	304 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	305 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	306 .. _help site: https://deeptools.readthedocs.org/
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	307
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	308 </token>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	309 <xml name="citations">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	310 <citations>
10 d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	311 <citation type="doi">10.1093/nar/gkw257</citation>
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	312 <yield />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	313 </citations>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	314 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	315
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	316 <xml name="multiple_input_bams">
5 511b69186073 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	317 <param argument="--bamfiles" type="data" format="bam" min="1"
511b69186073 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	318 label="Bam file" multiple="true"
7 5c4660838326 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c bgruening parents: 5 diff changeset	319 help=""/>
5 511b69186073 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	320 </xml>
511b69186073 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	321
511b69186073 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	322 <xml name="multiple_input_bams_min2">
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	323 <param argument="--bamfiles" type="data" format="bam" min="2"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	324 label="Bam file" multiple="true"
7 5c4660838326 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c bgruening parents: 5 diff changeset	325 help=""/>
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	326 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	327
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	328 <xml name="multiple_input_bigwigs">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	329 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	330 label="Bigwig file"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	331 help="A Bigwig file."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	332 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	333
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	334 <xml name="plotTitle">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	335 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	336 label="Title of the plot"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	337 help="Title of the plot, to be printed on top of the generated image." />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	338 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	339
4 30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	340
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	341 <token name="@multiple_input_bams@">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	342 <![CDATA[
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	343 #set files=[]
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	344 #set labels=[]
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	345 #for $counter, $bamfile in enumerate($bamfiles):
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	346 ln -s "${bamfile}" "./${counter}.bam" &&
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	347 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	348 #silent $files.append('%s.bam' % $counter)
9 9a16cdd40ef6 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356 bgruening parents: 7 diff changeset	349 #silent $labels.append("'%s'" % ($bamfile.display_name))
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	350 #end for
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	351 ]]>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	352 </token>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	353
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	354 <token name="@multiple_input_bigwigs@">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	355 <![CDATA[
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	356 #set files=[]
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	357 #set labels=[]
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	358 #for $counter, $bigwig in enumerate($bigwigfiles):
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	359 ln -s "${bigwig}" "${counter}.bw" &&
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	360 #silent $files.append('%s.bw' % $counter)
9 9a16cdd40ef6 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356 bgruening parents: 7 diff changeset	361 #silent $labels.append("'%s'" % ($bigwig.display_name))
0 bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	362 #end for
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	363 ]]>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	364 </token>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	365
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	366 <xml name="reference_genome_source">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	367 <conditional name="source">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	368 <param name="ref_source" type="select" label="Reference genome">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	369 <option value="cached">locally cached</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	370 <option value="history">in your history</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	371 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	372 <when value="cached">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	373 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	374 <options from_data_table="lastz_seqs">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	375 <filter type="sort_by" column="1" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	376 <validator type="no_options" message="No indexes are available." />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	377 </options>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	378 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	379 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	380 <when value="history">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	381 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	382 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	383 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	384 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	385
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	386 <token name="@reference_genome_source@">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	387 #if $source.ref_source=="history":
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	388 --genome $source.input1
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	389 #else:
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	390 --genome "$source.input1_2bit.fields.path"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	391 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	392 </token>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	393
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	394 <xml name="effectiveGenomeSize">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	395 <conditional name="effectiveGenomeSize">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	396 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	397 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.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	398 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	399 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.">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	400 <option value="93260000">ce10 (93260000)</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	401 <option value="121400000">dm3 (121400000)</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	402 <option value="2451960000" selected="true">hg19 (2451960000)</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	403 <option value="2150570000">mm9 (2150570000)</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	404 <option value="specific">user specified</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	405 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	406 <when value="specific">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	407 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	408 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	409 <when value="2150570000" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	410 <when value="2451960000" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	411 <when value="121400000" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	412 <when value="93260000" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	413 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	414 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	415
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	416 <xml name="skipNAs">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	417 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	418 label="Ignore missing data?"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	419 help="This parameter determines if non-covered regions
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	420 (regions without overlapping reads) in a bam/bigWig file
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	421 should be skipped. The default is to treat those
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	422 regions as having a value of zero. The decision to
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	423 skip non-covered regions depends on the interpretation
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	424 of the data. Non-covered regions may represent, for
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	425 example, repetitive regions that should be ignored.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	426 (default: False)" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	427 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	428
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	429 <xml name="input_save_matrix_values">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	430 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	431 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	432
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	433 <xml name="input_graphic_output_settings">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	434 <conditional name="output" >
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	435 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	436 <option value="no" selected="true">no</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	437 <option value="yes">yes</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	438 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	439 <when value="no" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	440 <when value="yes">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	441 <yield />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	442 <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."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	443 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	444 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	445 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	446
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	447
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	448 <xml name="input_image_file_format">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	449 <param argument="--outFileFormat" type="select" label="Image file format">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	450 <option value="png" selected="true">png</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	451 <option value="pdf">pdf</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	452 <option value="svg">svg</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	453 <option value="eps">eps</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	454 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	455 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	456
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	457 <xml name="output_image_file_format">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	458 <data format="png" name="outFileName" label="${tool.name} image">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	459 <change_format>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	460 <when input="output.outFileFormat" value="pdf" format="pdf" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	461 <when input="output.outFileFormat" value="svg" format="svg" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	462 <when input="output.outFileFormat" value="eps" format="eps" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	463 </change_format>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	464 </data>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	465 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	466
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	467 <xml name="output_image_file_format_not_nested">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	468 <data format="png" name="outFileName" label="${tool.name} image">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	469 <change_format>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	470 <when input="outFileFormat" value="pdf" format="pdf" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	471 <when input="outFileFormat" value="svg" format="svg" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	472 <when input="outFileFormat" value="eps" format="eps" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	473 </change_format>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	474 </data>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	475 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	476
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	477 <xml name="output_save_matrix_values">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	478 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	479 <filter>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	480 ((
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	481 output['showOutputSettings'] == 'yes' and
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	482 output['saveMatrix'] is True
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	483 ))
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	484 </filter>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	485 </data>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	486 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	487
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	488 <xml name="output_graphic_outputs">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	489 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	490 <filter>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	491 ((
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	492 output['showOutputSettings'] == 'yes' and
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	493 output['saveSortedRegions'] is True
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	494 ))
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	495 </filter>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	496 </data>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	497 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	498
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	499 <xml name="colorMap">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	500 <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/">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	501 <option value="RdYlBu" selected="true">RdYlBu</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	502 <option value="Accent">Accent</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	503 <option value="Spectral">Spectral</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	504 <option value="Set1">Set1</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	505 <option value="Set2">Set2</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	506 <option value="Set3">Set3</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	507 <option value="Dark2">Dark2</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	508 <option value="Reds">Reds</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	509 <option value="Oranges">Oranges</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	510 <option value="Greens">Greens</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	511 <option value="Blues">Blues</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	512 <option value="Greys">Greys</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	513 <option value="Purples">Purples</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	514 <option value="Paired">Paired</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	515 <option value="Pastel1">Pastel1</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	516 <option value="Pastel2">Pastel2</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	517 <option value="spring">spring</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	518 <option value="summer">summer</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	519 <option value="autumn">autumn</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	520 <option value="winter">winter</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	521 <option value="hot">hot</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	522 <option value="coolwarm">coolwarm</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	523 <option value="cool">cool</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	524 <option value="seismic">seismic</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	525 <option value="terrain">terrain</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	526 <option value="ocean">ocean</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	527 <option value="rainbow">rainbow</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	528 <option value="bone">bone</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	529 <option value="flag">flag</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	530 <option value="prism">prism</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	531 <option value="cubehelix">cubehelix</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	532 <option value="binary">binary</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	533 <option value="pink">pink</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	534 <option value="gray">gray</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	535 <option value="copper">copper</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	536 <option value="BrBG">BrBG</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	537 <option value="BuGn">BuGn</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	538 <option value="BuPu">BuPu</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	539 <option value="GnBu">GnBu</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	540 <option value="OrRd">OrRd</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	541 <option value="PiYG">PiYG</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	542 <option value="PRGn">PRGn</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	543 <option value="PuOr">PuOr</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	544 <option value="PuRd">PuRd</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	545 <option value="PuBu">PuBu</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	546 <option value="RdBu">RdBu</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	547 <option value="RdGy">RdGy</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	548 <option value="RdPu">RdPu</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	549 <option value="YlGn">YlGn</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	550 <option value="PuBuGn">PuBuGn</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	551 <option value="RdYlGn">RdYlGn</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	552 <option value="YlGnBu">YlGnBu</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	553 <option value="YlOrBr">YlOrBr</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	554 <option value="YlOrRd">YlOrRd</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	555 <option value="gist_gray">gist_gray</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	556 <option value="gist_stern">gist_stern</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	557 <option value="gist_earth">gist_earth</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	558 <option value="gist_yarg">gist_yarg</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	559 <option value="gist_ncar">gist_ncar</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	560 <option value="gist_rainbow">gist_rainbow</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	561 <option value="gist_heat">gist_heat</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	562 <option value="gnuplot">gnuplot</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	563 <option value="gnuplot2">gnuplot2</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	564 <option value="CMRmap">CMRmap</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	565 <option value="bwr">bwr</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	566 <option value="hsv">hsv</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	567 <option value="brg">brg</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	568 <option value="jet">jet</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	569 <option value="afmhot">afmhot</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	570 <option value="Accent_r">Accent reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	571 <option value="Spectral_r">Spectral reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	572 <option value="Set1_r">Set1 reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	573 <option value="Set2_r">Set2 reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	574 <option value="Set3_r">Set3 reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	575 <option value="Dark2_r">Dark2 reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	576 <option value="Reds_r">Reds reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	577 <option value="Oranges_r">Oranges reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	578 <option value="Greens_r">Greens reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	579 <option value="Blues_r">Blues reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	580 <option value="Greys_r">Greys reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	581 <option value="Purples_r">Purples reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	582 <option value="Paired_r">Paired reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	583 <option value="Pastel1_r">Pastel1 reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	584 <option value="Pastel2_r">Pastel2 reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	585 <option value="spring_r">spring reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	586 <option value="summer_r">summer reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	587 <option value="autumn_r">autumn reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	588 <option value="winter_r">winter reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	589 <option value="hot_r">hot reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	590 <option value="coolwarm_r">coolwarm reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	591 <option value="cool_r">cool reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	592 <option value="seismic_r">seismic reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	593 <option value="terrain_r">terrain reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	594 <option value="ocean_r">ocean reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	595 <option value="rainbow_r">rainbow reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	596 <option value="bone_r">bone reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	597 <option value="flag_r">flag reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	598 <option value="prism_r">prism reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	599 <option value="cubehelix_r">cubehelix reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	600 <option value="binary_r">binary reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	601 <option value="pink_r">pink reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	602 <option value="gray_r">gray reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	603 <option value="copper_r">copper reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	604 <option value="BrBG_r">BrBG reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	605 <option value="BuGn_r">BuGn reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	606 <option value="BuPu_r">BuPu reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	607 <option value="GnBu_r">GnBu reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	608 <option value="OrRd_r">OrRd reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	609 <option value="PiYG_r">PiYG reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	610 <option value="PRGn_r">PRGn reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	611 <option value="PuOr_r">PuOr reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	612 <option value="PuRd_r">PuRd reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	613 <option value="PuBu_r">PuBu reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	614 <option value="RdBu_r">RdBu reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	615 <option value="RdGy_r">RdGy reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	616 <option value="RdPu_r">RdPu reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	617 <option value="YlGn_r">YlGn reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	618 <option value="PuBuGn_r">PuBuGn reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	619 <option value="RdYlBu_r">RdYlBu reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	620 <option value="RdYlGn_r">RdYlGn reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	621 <option value="YlGnBu_r">YlGnBu reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	622 <option value="YlOrBr_r">YlOrBr reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	623 <option value="YlOrRd_r">YlOrRd reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	624 <option value="gist_gray_r">gist_gray reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	625 <option value="gist_stern_r">gist_stern reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	626 <option value="gist_earth_r">gist_earth reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	627 <option value="gist_yarg_r">gist_yarg reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	628 <option value="gist_ncar_r">gist_ncar reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	629 <option value="gist_rainbow_r">gist_rainbow reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	630 <option value="gist_heat_r">gist_heat reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	631 <option value="gnuplot_r">gnuplot reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	632 <option value="gnuplot2_r">gnuplot2 reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	633 <option value="CMRmap_r">CMRmap reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	634 <option value="bwr_r">bwr reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	635 <option value="hsv_r">hsv reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	636 <option value="brg_r">brg reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	637 <option value="jet_r">jet reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	638 <option value="afmhot_r">afmhot reversed</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	639 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	640
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	641 </xml>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	642
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	643 </macros>

Mercurial > repos > bgruening > deeptools_plot_fingerprint

annotate deepTools_macros.xml @ 10:d0a10af43611 draft