deeptools_bam_fingerprint: deepTools

annotate deepTools_macros.xml @ 7:b97024fb9c9f draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

author	bgruening
date	Wed, 23 Dec 2015 07:31:18 -0500
parents	cb90587dfd3a
children	ab153e5b5428

rev	line source
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	1 <macros>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	2
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	3 <xml name="advancedOpt_scaffold">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	4 <conditional name="advancedOpt">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	6 <option value="no" selected="true">no</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	7 <option value="yes">yes</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	8 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	9 <when value="no" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	10 <when value="yes">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	11 <yield/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	12 </when>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	13 </conditional>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	14 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	15
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	20 --extendReads
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	21 #end if
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	23 $advancedOpt.centerReads
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	26 #end if
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	29 #end if
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	32 #end if
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	33 </token>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	34
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	35 <xml name="heatmap_options">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	36 <expand macro="zMin_zMax" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	37 <expand macro="colorMap" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	38 <expand macro="plotTitle" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	39 <expand macro="plotNumbers" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	40 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	41
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	42 <token name="@HEATMAP_OPTIONS@">
7 b97024fb9c9f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	43 #if str($plotting_type.zMin) != "":
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	44 --zMin $plotting_type.zMin
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	45 #end if
7 b97024fb9c9f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	46 #if str($plotting_type.zMax) != "":
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	47 --zMax $plotting_type.zMax
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	48 #end if
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	49 --colorMap '$plotting_type.colorMap'
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	50 $plotting_type.plotNumbers
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	51 --plotTitle '$plotting_type.plotTitle'
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	52 </token>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	53
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	54
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	55 <xml name="includeZeros">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	57 label="Include zeros"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	58 help="If set, then regions with zero counts for all BAM files given are included. The default behavior is to ignore those cases." />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	59 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	60
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	61 <xml name="zMin_zMax">
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	63 help="If not specified the value is set automatically."/>
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	65 help="If not specified the value is set automatically."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	66 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	67
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	68 <xml name="region_limit_operation">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	69 <param argument="--region" type="text" value=""
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	70 label="Region of the genome to limit the operation to"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	71 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	72 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	73
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
1 4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	75 <token name="@WRAPPER_VERSION@">2.0.0</token>
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	76 <xml name="requirements">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	77 <requirements>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	78 <requirement type="package" version="2.7.10">python</requirement>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	79 <requirement type="binary">@BINARY@</requirement>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	80 <requirement type="package" version="2.0">deepTools</requirement>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	81 <yield />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	82 </requirements>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	83 <expand macro="stdio" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	84 <version_command>@BINARY@ --version</version_command>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	85 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	86
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	87 <xml name="smoothLength">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	88 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	89 label="Smooth values using the following length (in bp)"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	90 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	91 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	92
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	93
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	94 <xml name="kmeans_clustering">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	95 <conditional name="used_multiple_regions">
2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	96 <param name="used_multiple_regions_options" type="select"
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	97 label="Did you compute the matrix with more than one groups of regions?"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	98 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	99 <option value="yes">Yes, I used multiple groups of regions</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	100 <option value="no">No, I used only one group</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	101 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	102 <when value="no">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	103 <conditional name="clustering">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	104 <param name="clustering_options" type="select" label="Clustering algorithm">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	105 <option value="none">No clustering</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	106 <option value="kmeans">Kmeans clustering</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	107 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	108 <when value="kmeans">
2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	109 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
7 b97024fb9c9f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	110 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm.
b97024fb9c9f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	111 Only works for data that is not grouped, otherwise only the first group will be clustered.
b97024fb9c9f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	112 If more specific clustering methods are required it is advisable to save the underlying matrix and
b97024fb9c9f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	113 run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault)
b97024fb9c9f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	114 if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/>
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	115 </when>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	116 <when value="none" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	117 </conditional>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	118 </when>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	119 <when value="yes" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	120 </conditional>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	121 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	122
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	123 <token name="@KMEANS_CLUSTERING@">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	124 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	125 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	126 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	127 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	128 #end if
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	129 #end if
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	130 #end if
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	131 </token>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	132
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	133 <xml name="samFlags">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	134 <param argument="--samFlagInclude" type="integer" optional="True" value=""
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	135 label="Include reads based on the SAM flag"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	136 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."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	137 <param argument="--samFlagExclude" type="integer" optional="True" value=""
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	138 label="Exclude reads based on the SAM flag"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	139 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."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	140 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	141
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	142 <xml name="read_processing_options">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	143 <expand macro="extendReads" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	144 <expand macro="ignoreDuplicates" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	145 <expand macro="centerReads" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	146 <expand macro="minMappingQuality" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	147 <expand macro="samFlags" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	148 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	149
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	150 <xml name="plotNumbers">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	151 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	152 label="Plot the correlation value"
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	153 help="If set, then the correlation number is plotted on top of the heatmap."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	154 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	155
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	156 <xml name="extendReads">
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	157 <conditional name="doExtendCustom">
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	158 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	159 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.
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	160 By default each read mate is extended.
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	161 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	162 Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	163 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
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	164 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	165 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	166 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	167 <option value="custom">A custom length, which will be applied to ALL reads.</option>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	168 </param>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	169 <when value="no" />
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	170 <when value="yes" />
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	171 <when value="custom">
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	172 <param name="extendReadsValue" type="integer" value="300" min="1"
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	173 label="Extend reads to the given average fragment size"
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	174 help="Extend all reads to this length" />
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	175 </when>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	176 </conditional>
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	177 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	178
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	179 <xml name="corMethod">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	180 <param argument="--corMethod" type="select" label="Correlation method">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	181 <option value="spearman" selected="True">Spearman</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	182 <option value="pearson">Pearson</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	183 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	184 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	185
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	186 <xml name="distanceBetweenBins">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	187 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	188 label="Distance between bins"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	189 help="By default, bamCorrelate considers consecutive bins of
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	190 the specified 'Bin size'. However, to reduce the
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	191 computation time, a larger distance between bins can
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	192 by given. Larger distances result in less bins being
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	193 considered."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	194 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	195
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	196 <xml name="centerReads">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	197 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	198 label="Center regions with respect to the fragment length"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	199 help="For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. "/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	200 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	201
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	202 <xml name="ignoreDuplicates">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	203 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	204 label="Ignore duplicates"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	205 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." />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	206 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	207
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	208 <xml name="sortUsing">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	209 <param argument="--sortUsing" type="select" label="Method used for sorting"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	210 help="For each row the method is computed.">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	211 <option value="mean" selected="true">mean</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	212 <option value="median">median</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	213 <option value="min">min</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	214 <option value="max">max</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	215 <option value="sum">sum</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	216 <option value="region_length">region length</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	217 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	218 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	219
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	220 <xml name="sortRegions">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	221 <param argument="--sortRegions" type="select" label="Sort regions"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	222 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	223 <option value="no">no ordering</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	224 <option value="descend" selected="true">descending order</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	225 <option value="ascend">ascending order</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	226 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	227 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	228
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	229 <xml name="minMappingQuality">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	230 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	231 label="Minimum mapping quality"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	232 help= "If set, only reads that have a mapping quality score higher than the given value are considered. Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	233 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	234
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	235 <xml name="skipZeros">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	236 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	237 label ="Skip zeros"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	238 help ="If set, then zero counts that happen for all BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	239 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	240
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	241 <xml name="fragmentLength">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	242 <param argument="--fragmentLength" type="integer" value="300" min="1"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	243 label="Fragment length used for the sequencing"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	244 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	245 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	246
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	247 <xml name="scaleFactor">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	248 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	249 help="When used in combination with --normalizeTo1x or
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	250 --normalizeUsingRPKM, the computed scaling factor will
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	251 be multiplied by the given scale factor." />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	252 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	253
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	254 <xml name="scaleFactors">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	255 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	256 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	257 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	258
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	259 <xml name="stdio">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	260 <stdio>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	261 <exit_code range="1:" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	262 <exit_code range=":-1" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	263 <regex match="Error:" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	264 <regex match="Exception:" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	265 <regex match="EXception:" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	266 <regex match="Traceback" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	267 </stdio>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	268 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	269
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	270 <xml name="pseudocount">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	271 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	272 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	273
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	274 <token name="@REFERENCES@">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	275
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	276 .. class:: infomark
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	277
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	278 For more information on the tools, please visit our `help site`_.
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	279
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	280 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	281
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	282 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	284 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	285 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	286 .. _help site: https://deeptools.readthedocs.org/
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	287
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	289 <xml name="citations">
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	291 <citation type="doi">10.1093/nar/gku365</citation>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	292 <yield />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	293 </citations>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	294 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	295
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3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	297 <param argument="--bamfiles" type="data" format="bam" min="2"
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	298 label="Bam file" multiple="true"
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	300 </xml>
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3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	303 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	304 label="Bigwig file"
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	305 help="The Bigwig file must be sorted."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	306 </xml>
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	308 <xml name="plotTitle">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	309 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	310 label="Title of the plot"
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	311 help="Title of the plot, to be printed on top of the generated image." />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	312 </xml>
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	315 <![CDATA[
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	316 #set files=[]
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	317 #set labels=[]
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	318 #for $counter, $bamfile in enumerate($bamfiles):
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	319 ln -s "${bamfile}" "./${counter}.bam" &&
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	320 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	321 #silent $files.append('%s.bam' % $counter)
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	322 #silent $labels.append('%s' % ($bamfile.display_name))
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	323 #end for
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	324 ]]>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	325 </token>
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	328 <![CDATA[
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	329 #set files=[]
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	330 #set labels=[]
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	331 #for $counter, $bigwig in enumerate($bigwigfiles):
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	332 ln -s "${bigwig}" "${counter}.bw" &&
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	333 #silent $files.append('%s.bw' % $counter)
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	334 #silent $labels.append('%s' % ($bigwig.display_name))
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	335 #end for
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	336 ]]>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	337 </token>
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	340 <conditional name="source">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	341 <param name="ref_source" type="select" label="Reference genome">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	342 <option value="cached">locally cached</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	343 <option value="history">in your history</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	344 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	345 <when value="cached">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	346 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	347 <options from_data_table="lastz_seqs">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	348 <filter type="sort_by" column="1" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	349 <validator type="no_options" message="No indexes are available." />
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	353 <when value="history">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	354 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	355 </when>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	356 </conditional>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	357 </xml>
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3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	359 <token name="@reference_genome_source@">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	360 #if $source.ref_source=="history":
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	361 --genome $source.input1
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	362 #else:
4 73daabb6c01e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: 3 diff changeset	363 --genome "$source.input1_2bit.fields.path"
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	364 #end if
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	365 </token>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	366
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	367 <xml name="effectiveGenomeSize">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	368 <conditional name="effectiveGenomeSize">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	369 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	370 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.
480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	371 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	372 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.">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	373 <option value="93260000">ce10 (93260000)</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	374 <option value="121400000">dm3 (121400000)</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	375 <option value="2451960000" selected="true">hg19 (2451960000)</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	376 <option value="2150570000">mm9 (2150570000)</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	377 <option value="specific">user specified</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	378 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	379 <when value="specific">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	380 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	381 </when>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	382 <when value="2150570000" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	383 <when value="2451960000" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	384 <when value="121400000" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	385 <when value="93260000" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	386 </conditional>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	387 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	388
1 4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	389 <xml name="skipNAs">
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	390 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	391 label="Ignore missing data?"
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	392 help="This parameter determines if non-covered regions
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	393 (regions without overlapping reads) in a bam/bigWig file
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	394 should be skipped. The default is to treat those
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	395 regions as having a value of zero. The decision to
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	396 skip non-covered regions depends on the interpretation
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	397 of the data. Non-covered regions may represent for
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	398 example repetitive regions that want to be skipped.
4935689a29ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	399 (default: False)" />
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	400 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	401
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	402 <xml name="input_save_matrix_values">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	403 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	404 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	405
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	406 <xml name="input_graphic_output_settings">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	407 <conditional name="output" >
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	408 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	409 <option value="no" selected="true">no</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	410 <option value="yes">yes</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	411 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	412 <when value="no" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	413 <when value="yes">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	414 <yield />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	415 <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."/>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	416 </when>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	417 </conditional>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	418 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	419
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	420
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	421 <xml name="input_image_file_format">
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	422 <param argument="--outFileFormat" type="select" label="Image file format">
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	423 <option value="png" selected="true">png</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	424 <option value="pdf">pdf</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	425 <option value="svg">svg</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	426 <option value="eps">eps</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	427 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	428 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	429
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	430 <xml name="output_image_file_format">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	431 <data format="png" name="outFileName" label="${tool.name} image">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	432 <change_format>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	433 <when input="output.outFileFormat" value="pdf" format="pdf" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	434 <when input="output.outFileFormat" value="svg" format="svg" />
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	435 <when input="output.outFileFormat" value="eps" format="eps" />
3 63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	436 </change_format>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	437 </data>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	438 </xml>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	439
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	440 <xml name="output_image_file_format_not_nested">
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	441 <data format="png" name="outFileName" label="${tool.name} image">
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	442 <change_format>
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	443 <when input="outFileFormat" value="pdf" format="pdf" />
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	444 <when input="outFileFormat" value="svg" format="svg" />
63947275d189 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	445 <when input="outFileFormat" value="eps" format="eps" />
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	446 </change_format>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	447 </data>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	448 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	449
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	450 <xml name="output_save_matrix_values">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	451 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	452 <filter>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	453 ((
2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	454 output['showOutputSettings'] == 'yes' and
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	455 output['saveMatrix'] is True
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	456 ))
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	457 </filter>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	458 </data>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	459 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	460
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	461 <xml name="output_graphic_outputs">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	462 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	463 <filter>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	464 ((
2 480d812763d2 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	465 output['showOutputSettings'] == 'yes' and
0 3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	466 output['saveSortedRegions'] is True
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	467 ))
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	468 </filter>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	469 </data>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	470 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	471
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	472 <xml name="colorMap">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	473 <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/">
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	474 <option value="RdYlBu" selected="true">RdYlBu</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	475 <option value="Accent">Accent</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	476 <option value="Spectral">Spectral</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	477 <option value="Set1">Set1</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	478 <option value="Set2">Set2</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	479 <option value="Set3">Set3</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	480 <option value="Dark2">Dark2</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	481 <option value="Reds">Reds</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	482 <option value="Oranges">Oranges</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	483 <option value="Greens">Greens</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	484 <option value="Blues">Blues</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	485 <option value="Greys">Greys</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	486 <option value="Purples">Purples</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	487 <option value="Paired">Paired</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	488 <option value="Pastel1">Pastel1</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	489 <option value="Pastel2">Pastel2</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	490 <option value="spring">spring</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	491 <option value="summer">summer</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	492 <option value="autumn">autumn</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	493 <option value="winter">winter</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	494 <option value="hot">hot</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	495 <option value="coolwarm">coolwarm</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	496 <option value="cool">cool</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	497 <option value="seismic">seismic</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	498 <option value="terrain">terrain</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	499 <option value="ocean">ocean</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	500 <option value="rainbow">rainbow</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	501 <option value="bone">bone</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	502 <option value="flag">flag</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	503 <option value="prism">prism</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	504 <option value="cubehelix">cubehelix</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	505 <option value="binary">binary</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	506 <option value="pink">pink</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	507 <option value="gray">gray</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	508 <option value="copper">copper</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	509 <option value="BrBG">BrBG</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	510 <option value="BuGn">BuGn</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	511 <option value="BuPu">BuPu</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	512 <option value="GnBu">GnBu</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	513 <option value="OrRd">OrRd</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	514 <option value="PiYG">PiYG</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	515 <option value="PRGn">PRGn</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	516 <option value="PuOr">PuOr</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	517 <option value="PuRd">PuRd</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	518 <option value="PuBu">PuBu</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	519 <option value="RdBu">RdBu</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	520 <option value="RdGy">RdGy</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	521 <option value="RdPu">RdPu</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	522 <option value="YlGn">YlGn</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	523 <option value="PuBuGn">PuBuGn</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	524 <option value="RdYlGn">RdYlGn</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	525 <option value="YlGnBu">YlGnBu</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	526 <option value="YlOrBr">YlOrBr</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	527 <option value="YlOrRd">YlOrRd</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	528 <option value="gist_gray">gist_gray</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	529 <option value="gist_stern">gist_stern</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	530 <option value="gist_earth">gist_earth</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	531 <option value="gist_yarg">gist_yarg</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	532 <option value="gist_ncar">gist_ncar</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	533 <option value="gist_rainbow">gist_rainbow</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	534 <option value="gist_heat">gist_heat</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	535 <option value="gnuplot">gnuplot</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	536 <option value="gnuplot2">gnuplot2</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	537 <option value="CMRmap">CMRmap</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	538 <option value="bwr">bwr</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	539 <option value="hsv">hsv</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	540 <option value="brg">brg</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	541 <option value="jet">jet</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	542 <option value="afmhot">afmhot</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	543 <option value="Accent_r">Accent reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	544 <option value="Spectral_r">Spectral reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	545 <option value="Set1_r">Set1 reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	546 <option value="Set2_r">Set2 reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	547 <option value="Set3_r">Set3 reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	548 <option value="Dark2_r">Dark2 reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	549 <option value="Reds_r">Reds reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	550 <option value="Oranges_r">Oranges reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	551 <option value="Greens_r">Greens reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	552 <option value="Blues_r">Blues reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	553 <option value="Greys_r">Greys reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	554 <option value="Purples_r">Purples reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	555 <option value="Paired_r">Paired reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	556 <option value="Pastel1_r">Pastel1 reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	557 <option value="Pastel2_r">Pastel2 reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	558 <option value="spring_r">spring reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	559 <option value="summer_r">summer reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	560 <option value="autumn_r">autumn reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	561 <option value="winter_r">winter reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	562 <option value="hot_r">hot reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	563 <option value="coolwarm_r">coolwarm reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	564 <option value="cool_r">cool reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	565 <option value="seismic_r">seismic reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	566 <option value="terrain_r">terrain reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	567 <option value="ocean_r">ocean reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	568 <option value="rainbow_r">rainbow reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	569 <option value="bone_r">bone reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	570 <option value="flag_r">flag reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	571 <option value="prism_r">prism reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	572 <option value="cubehelix_r">cubehelix reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	573 <option value="binary_r">binary reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	574 <option value="pink_r">pink reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	575 <option value="gray_r">gray reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	576 <option value="copper_r">copper reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	577 <option value="BrBG_r">BrBG reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	578 <option value="BuGn_r">BuGn reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	579 <option value="BuPu_r">BuPu reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	580 <option value="GnBu_r">GnBu reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	581 <option value="OrRd_r">OrRd reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	582 <option value="PiYG_r">PiYG reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	583 <option value="PRGn_r">PRGn reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	584 <option value="PuOr_r">PuOr reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	585 <option value="PuRd_r">PuRd reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	586 <option value="PuBu_r">PuBu reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	587 <option value="RdBu_r">RdBu reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	588 <option value="RdGy_r">RdGy reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	589 <option value="RdPu_r">RdPu reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	590 <option value="YlGn_r">YlGn reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	591 <option value="PuBuGn_r">PuBuGn reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	592 <option value="RdYlBu_r">RdYlBu reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	593 <option value="RdYlGn_r">RdYlGn reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	594 <option value="YlGnBu_r">YlGnBu reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	595 <option value="YlOrBr_r">YlOrBr reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	596 <option value="YlOrRd_r">YlOrRd reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	597 <option value="gist_gray_r">gist_gray reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	598 <option value="gist_stern_r">gist_stern reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	599 <option value="gist_earth_r">gist_earth reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	600 <option value="gist_yarg_r">gist_yarg reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	601 <option value="gist_ncar_r">gist_ncar reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	602 <option value="gist_rainbow_r">gist_rainbow reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	603 <option value="gist_heat_r">gist_heat reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	604 <option value="gnuplot_r">gnuplot reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	605 <option value="gnuplot2_r">gnuplot2 reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	606 <option value="CMRmap_r">CMRmap reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	607 <option value="bwr_r">bwr reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	608 <option value="hsv_r">hsv reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	609 <option value="brg_r">brg reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	610 <option value="jet_r">jet reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	611 <option value="afmhot_r">afmhot reversed</option>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	612 </param>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	613
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	614 </xml>
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	615
3d29a3c9cdab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	616 </macros>

Mercurial > repos > bgruening > deeptools_bam_fingerprint

annotate deepTools_macros.xml @ 7:b97024fb9c9f draft