deeptools_plot_correlation: deepTools

annotate deepTools_macros.xml @ 1:08b01bdab227 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427

author	bgruening
date	Fri, 18 Dec 2015 08:00:49 -0500
parents	b0050909cf03
children	c5634baf9bf9

rev	line source
0 b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	1 <macros>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	2
b0050909cf03 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">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	4 <conditional name="advancedOpt">
b0050909cf03 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" >
b0050909cf03 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>
b0050909cf03 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>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	8 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	9 <when value="no" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	10 <when value="yes">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	11 <yield/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	12 </when>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	13 </conditional>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	14 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	15
b0050909cf03 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@">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	17 --extendReads $advancedOpt.extendReads
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	18 $advancedOpt.ignoreDuplicates
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	19 $advancedOpt.centerReads
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	20 #if $advancedOpt.minMappingQuality:
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	21 --minMappingQuality '$advancedOpt.minMappingQuality'
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	22 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	23 #if $advancedOpt.samFlagInclude:
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	24 --samFlagInclude $advancedOpt.samFlagInclude
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	25 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	26 #if $advancedOpt.samFlagExclude:
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	27 --samFlagExclude $advancedOpt.samFlagExclude
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	28 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	29 </token>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	30
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	31 <xml name="heatmap_options">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	32 <expand macro="zMin_zMax" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	33 <expand macro="colorMap" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	34 <expand macro="plotTitle" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	35 <expand macro="plotNumbers" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	36 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	37
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	38 <token name="@HEATMAP_OPTIONS@">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	39 #if $zMin:
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	40 --zMin $zMin
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	41 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	42 #if $zMax:
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	43 --zMax $zMax
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	44 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	45 --colorMap '$colorMap'
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	46 $plotNumbers
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	47 </token>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	48
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	49 <expand macro="plotTitle" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	50 <expand macro="plotNumbers" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	51 <conditional name="output">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	52 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	53 <option value="no" selected="true">no</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	54 <option value="yes">yes</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	55 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	56 <when value="no" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	57 <when value="yes">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	58 <expand macro="input_image_file_format"/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	59 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	60 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	61 </when>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	62 </conditional>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	63
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	64 <xml name="includeZeros">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	65 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	66 label="Include zeros"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	67 help="If set, then regions with zero counts for all BAM files given are included. The default behavior is to ignore those cases." />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	68 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	69
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	70 <xml name="zMin_zMax">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	71 <param argument="--zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	72 help="If not specified the value is set automatically."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	73 <param argument="--zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	74 help="If not specified the value is set automatically."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	75 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	76
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	77 <xml name="region_limit_operation">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	78 <param argument="--region" type="text" value=""
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	79 label="Region of the genome to limit the operation to"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	80 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"." />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	81 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	82
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	83 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
1 08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	84 <token name="@WRAPPER_VERSION@">2.0.0</token>
0 b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	85 <xml name="requirements">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	86 <requirements>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	87 <requirement type="package" version="2.7.10">python</requirement>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	88 <requirement type="binary">@BINARY@</requirement>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	89 <requirement type="package" version="2.0">deepTools</requirement>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	90 <yield />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	91 </requirements>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	92 <expand macro="stdio" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	93 <version_command>@BINARY@ --version</version_command>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	94 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	95
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	96 <xml name="smoothLength">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	97 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	98 label="Smooth values using the following length (in bp)"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	99 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."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	100 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	101
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	102
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	103 <xml name="kmeans_clustering">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	104 <conditional name="used_multiple_regions">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	105 <param name="used_multiple_regions_options" type="select"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	106 label="Did you compute the matrix with more than one groups of regions?"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	107 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.">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	108 <option value="yes">Yes, I used multiple groups of regions</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	109 <option value="no">No, I used only one group</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	110 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	111 <when value="no">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	112 <conditional name="clustering">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	113 <param name="clustering_options" type="select" label="Clustering algorithm">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	114 <option value="none">No clustering</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	115 <option value="kmeans">Kmeans clustering</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	116 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	117 <when value="kmeans">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	118 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	119 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	120 </when>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	121 <when value="none" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	122 </conditional>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	123 </when>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	124 <when value="yes" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	125 </conditional>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	126 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	127
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	128 <token name="@KMEANS_CLUSTERING@">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	129 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	130 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	131 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	132 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	133 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	134 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	135 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	136 </token>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	137
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	138 <xml name="samFlags">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	139 <param argument="--samFlagInclude" type="integer" optional="True" value=""
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	140 label="Include reads based on the SAM flag"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	141 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."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	142 <param argument="--samFlagExclude" type="integer" optional="True" value=""
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	143 label="Exclude reads based on the SAM flag"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	144 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."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	145 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	146
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	147 <xml name="read_processing_options">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	148 <expand macro="extendReads" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	149 <expand macro="ignoreDuplicates" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	150 <expand macro="centerReads" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	151 <expand macro="minMappingQuality" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	152 <expand macro="samFlags" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	153 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	154
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	155 <xml name="plotNumbers">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	156 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	157 label="Plot the correlation value"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	158 help="If set, then the correlation number is plotted on top of the heatmap."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	159 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	160
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	161 <xml name="extendReads">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	162 <param argument="--extendReads" type="integer" value="" optional="True"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	163 label="Extend reads to the given average fragment size"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	164 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.
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	165 By default each read mate is extended.
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	166 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	167 Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	168 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
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	169 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	170 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	171
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	172 <xml name="corMethod">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	173 <param argument="--corMethod" type="select" label="Correlation method">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	174 <option value="spearman" selected="True">Spearman</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	175 <option value="pearson">Pearson</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	176 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	177 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	178
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	179 <xml name="distanceBetweenBins">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	180 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	181 label="Distance between bins"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	182 help="By default, bamCorrelate considers consecutive bins of
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	183 the specified 'Bin size'. However, to reduce the
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	184 computation time, a larger distance between bins can
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	185 by given. Larger distances result in less bins being
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	186 considered."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	187 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	188
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	189 <xml name="centerReads">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	190 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	191 label="Center regions with respect to the fragment length"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	192 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. "/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	193 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	194
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	195 <xml name="ignoreDuplicates">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	196 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	197 label="Ignore duplicates"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	198 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." />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	199 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	200
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	201 <xml name="sortUsing">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	202 <param argument="--sortUsing" type="select" label="Method used for sorting"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	203 help="For each row the method is computed.">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	204 <option value="mean" selected="true">mean</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	205 <option value="median">median</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	206 <option value="min">min</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	207 <option value="max">max</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	208 <option value="sum">sum</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	209 <option value="region_length">region length</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	210 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	211 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	212
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	213 <xml name="sortRegions">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	214 <param argument="--sortRegions" type="select" label="Sort regions"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	215 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	216 <option value="no">no ordering</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	217 <option value="descend" selected="true">descending order</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	218 <option value="ascend">ascending order</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	219 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	220 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	221
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	222 <xml name="minMappingQuality">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	223 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	224 label="Minimum mapping quality"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	225 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."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	226 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	227
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	228 <xml name="skipZeros">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	229 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	230 label ="Skip zeros"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	231 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." />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	232 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	233
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	234 <xml name="fragmentLength">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	235 <param argument="--fragmentLength" type="integer" value="300" min="1"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	236 label="Fragment length used for the sequencing"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	237 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	238 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	239
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	240 <xml name="scaleFactor">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	241 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	242 help="When used in combination with --normalizeTo1x or
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	243 --normalizeUsingRPKM, the computed scaling factor will
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	244 be multiplied by the given scale factor." />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	245 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	246
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	247 <xml name="scaleFactors">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	248 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	249 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	250 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	251
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	252 <xml name="stdio">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	253 <stdio>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	254 <exit_code range="1:" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	255 <exit_code range=":-1" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	256 <regex match="Error:" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	257 <regex match="Exception:" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	258 <regex match="EXception:" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	259 <regex match="Traceback" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	260 </stdio>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	261 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	262
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	263 <xml name="pseudocount">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	264 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	265 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	266
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	267 <token name="@REFERENCES@">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	268
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	269 .. class:: infomark
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	270
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	271 For more information on the tools, please visit our `help site`_.
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	272
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	273 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	274
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	275 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	276
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	277 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	278 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	279 .. _help site: https://github.com/fidelram/deepTools/wiki/
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	280
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	281 </token>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	282 <xml name="citations">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	283 <citations>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	284 <citation type="doi">10.1093/nar/gku365</citation>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	285 <yield />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	286 </citations>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	287 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	288
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	289 <xml name="multiple_input_bams">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	290 <param argument="--bamfiles" type="data" format="bam"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	291 label="Bam file" multiple="true"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	292 help="The BAM file must be sorted."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	293 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	294
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	295 <xml name="multiple_input_bigwigs">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	296 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	297 label="Bigwig file"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	298 help="The Bigwig file must be sorted."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	299 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	300
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	301 <xml name="plotTitle">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	302 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	303 label="Title of the plot"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	304 help="Title of the plot, to be printed on top of the generated image." />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	305 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	306
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	307 <token name="@multiple_input_bams@">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	308 <![CDATA[
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	309 #set files=[]
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	310 #set labels=[]
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	311 #for $counter, $bamfile in enumerate($bamfiles):
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	312 ln -s "${bamfile}" "./${counter}.bam" &&
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	313 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	314 #silent $files.append('%s.bam' % $counter)
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	315 #silent $labels.append('%s' % ($bamfile.display_name))
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	316 #end for
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	317 ]]>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	318 </token>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	319
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	320 <token name="@multiple_input_bigwigs@">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	321 <![CDATA[
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	322 #set files=[]
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	323 #set labels=[]
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	324 #for $counter, $bigwig in enumerate($bigwigfiles):
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	325 ln -s "${bigwig}" "${counter}.bw" &&
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	326 #silent $files.append('%s.bw' % $counter)
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	327 #silent $labels.append('%s' % ($bigwig.display_name))
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	328 #end for
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	329 ]]>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	330 </token>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	331
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	332 <xml name="reference_genome_source">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	333 <conditional name="source">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	334 <param name="ref_source" type="select" label="Reference genome">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	335 <option value="cached">locally cached</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	336 <option value="history">in your history</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	337 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	338 <when value="cached">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	339 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	340 <options from_data_table="lastz_seqs">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	341 <filter type="sort_by" column="1" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	342 <validator type="no_options" message="No indexes are available." />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	343 </options>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	344 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	345 </when>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	346 <when value="history">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	347 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	348 </when>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	349 </conditional>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	350 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	351
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	352 <token name="@reference_genome_source@">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	353 #if $source.ref_source=="history":
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	354 --genome $source.input1
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	355 #else:
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	356 --genome "${source.input1_2bit.fields.path}"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	357 #end if
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	358 </token>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	359
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	360 <xml name="effectiveGenomeSize">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	361 <conditional name="effectiveGenomeSize">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	362 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	363 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.
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	364 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	365 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.">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	366 <option value="93260000">ce10 (93260000)</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	367 <option value="121400000">dm3 (121400000)</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	368 <option value="2451960000" selected="true">hg19 (2451960000)</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	369 <option value="2150570000">mm9 (2150570000)</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	370 <option value="specific">user specified</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	371 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	372 <when value="specific">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	373 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	374 </when>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	375 <when value="2150570000" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	376 <when value="2451960000" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	377 <when value="121400000" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	378 <when value="93260000" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	379 </conditional>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	380 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	381
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	382 <xml name="image_file_format">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	383 <param argument="--outFileFormat" type="select" label="Image file format">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	384 <option value="png" selected="true">png</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	385 <option value="pdf">pdf</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	386 <option value="svg">svg</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	387 <option value="eps">eps</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	388 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	389 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	390
1 08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	391 <xml name="skipNAs">
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	392 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	393 label="Ignore missing data?"
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	394 help="This parameter determines if non-covered regions
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	395 (regions without overlapping reads) in a bam/bigWig file
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	396 should be skipped. The default is to treat those
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	397 regions as having a value of zero. The decision to
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	398 skip non-covered regions depends on the interpretation
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	399 of the data. Non-covered regions may represent for
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	400 example repetitive regions that want to be skipped.
08b01bdab227 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	401 (default: False)" />
0 b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	402 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	403
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	404 <xml name="input_save_matrix_values">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	405 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	406 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	407
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	408 <xml name="input_graphic_output_settings">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	409 <conditional name="output" >
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	410 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	411 <option value="no" selected="true">no</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	412 <option value="yes">yes</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	413 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	414 <when value="no" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	415 <when value="yes">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	416 <yield />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	417 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	418 <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."/>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	419 </when>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	420 </conditional>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	421 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	422
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	423 <xml name="input_image_file_format">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	424 <param name="outFileFormat" type="select" label="Image file format">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	425 <option value="png" selected="true">png</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	426 <option value="pdf">pdf</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	427 <option value="svg">svg</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	428 <option value="eps">eps</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	429 <option value="emf">emf</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	430 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	431 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	432
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	433 <xml name="output_image_file_format">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	434 <data format="png" name="outFileName" label="${tool.name} image">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	435 <change_format>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	436 <when input="output.outFileFormat" value="pdf" format="pdf" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	437 <when input="output.outFileFormat" value="svg" format="svg" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	438 <when input="output.outFileFormat" value="eps" format="eps" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	439 <when input="output.outFileFormat" value="emf" format="emf" />
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	440 </change_format>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	441 </data>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	442 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	443
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	444 <xml name="output_save_matrix_values">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	445 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	446 <filter>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	447 ((
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	448 output['showOutputSettings'] == 'yes' and
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	449 output['saveMatrix'] is True
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	450 ))
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	451 </filter>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	452 </data>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	453 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	454
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	455 <xml name="output_graphic_outputs">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	456 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	457 <filter>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	458 ((
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	459 output['showOutputSettings'] == 'yes' and
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	460 output['saveData'] is True
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	461 ))
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	462 </filter>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	463 </data>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	464 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	465 <filter>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	466 ((
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	467 output['showOutputSettings'] == 'yes' and
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	468 output['saveSortedRegions'] is True
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	469 ))
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	470 </filter>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	471 </data>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	472 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	473
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	474 <xml name="colorMap">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	475 <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/">
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	476 <option value="RdYlBu" selected="true">RdYlBu</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	477 <option value="Accent">Accent</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	478 <option value="Spectral">Spectral</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	479 <option value="Set1">Set1</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	480 <option value="Set2">Set2</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	481 <option value="Set3">Set3</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	482 <option value="Dark2">Dark2</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	483 <option value="Reds">Reds</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	484 <option value="Oranges">Oranges</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	485 <option value="Greens">Greens</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	486 <option value="Blues">Blues</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	487 <option value="Greys">Greys</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	488 <option value="Purples">Purples</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	489 <option value="Paired">Paired</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	490 <option value="Pastel1">Pastel1</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	491 <option value="Pastel2">Pastel2</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	492 <option value="spring">spring</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	493 <option value="summer">summer</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	494 <option value="autumn">autumn</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	495 <option value="winter">winter</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	496 <option value="hot">hot</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	497 <option value="coolwarm">coolwarm</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	498 <option value="cool">cool</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	499 <option value="seismic">seismic</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	500 <option value="terrain">terrain</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	501 <option value="ocean">ocean</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	502 <option value="rainbow">rainbow</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	503 <option value="bone">bone</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	504 <option value="flag">flag</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	505 <option value="prism">prism</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	506 <option value="cubehelix">cubehelix</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	507 <option value="binary">binary</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	508 <option value="pink">pink</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	509 <option value="gray">gray</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	510 <option value="copper">copper</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	511 <option value="BrBG">BrBG</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	512 <option value="BuGn">BuGn</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	513 <option value="BuPu">BuPu</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	514 <option value="GnBu">GnBu</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	515 <option value="OrRd">OrRd</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	516 <option value="PiYG">PiYG</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	517 <option value="PRGn">PRGn</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	518 <option value="PuOr">PuOr</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	519 <option value="PuRd">PuRd</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	520 <option value="PuBu">PuBu</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	521 <option value="RdBu">RdBu</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	522 <option value="RdGy">RdGy</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	523 <option value="RdPu">RdPu</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	524 <option value="YlGn">YlGn</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	525 <option value="PuBuGn">PuBuGn</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	526 <option value="RdYlGn">RdYlGn</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	527 <option value="YlGnBu">YlGnBu</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	528 <option value="YlOrBr">YlOrBr</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	529 <option value="YlOrRd">YlOrRd</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	530 <option value="gist_gray">gist_gray</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	531 <option value="gist_stern">gist_stern</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	532 <option value="gist_earth">gist_earth</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	533 <option value="gist_yarg">gist_yarg</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	534 <option value="gist_ncar">gist_ncar</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	535 <option value="gist_rainbow">gist_rainbow</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	536 <option value="gist_heat">gist_heat</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	537 <option value="gnuplot">gnuplot</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	538 <option value="gnuplot2">gnuplot2</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	539 <option value="CMRmap">CMRmap</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	540 <option value="bwr">bwr</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	541 <option value="hsv">hsv</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	542 <option value="brg">brg</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	543 <option value="jet">jet</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	544 <option value="afmhot">afmhot</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	545 <option value="Accent_r">Accent reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	546 <option value="Spectral_r">Spectral reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	547 <option value="Set1_r">Set1 reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	548 <option value="Set2_r">Set2 reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	549 <option value="Set3_r">Set3 reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	550 <option value="Dark2_r">Dark2 reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	551 <option value="Reds_r">Reds reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	552 <option value="Oranges_r">Oranges reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	553 <option value="Greens_r">Greens reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	554 <option value="Blues_r">Blues reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	555 <option value="Greys_r">Greys reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	556 <option value="Purples_r">Purples reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	557 <option value="Paired_r">Paired reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	558 <option value="Pastel1_r">Pastel1 reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	559 <option value="Pastel2_r">Pastel2 reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	560 <option value="spring_r">spring reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	561 <option value="summer_r">summer reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	562 <option value="autumn_r">autumn reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	563 <option value="winter_r">winter reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	564 <option value="hot_r">hot reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	565 <option value="coolwarm_r">coolwarm reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	566 <option value="cool_r">cool reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	567 <option value="seismic_r">seismic reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	568 <option value="terrain_r">terrain reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	569 <option value="ocean_r">ocean reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	570 <option value="rainbow_r">rainbow reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	571 <option value="bone_r">bone reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	572 <option value="flag_r">flag reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	573 <option value="prism_r">prism reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	574 <option value="cubehelix_r">cubehelix reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	575 <option value="binary_r">binary reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	576 <option value="pink_r">pink reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	577 <option value="gray_r">gray reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	578 <option value="copper_r">copper reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	579 <option value="BrBG_r">BrBG reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	580 <option value="BuGn_r">BuGn reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	581 <option value="BuPu_r">BuPu reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	582 <option value="GnBu_r">GnBu reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	583 <option value="OrRd_r">OrRd reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	584 <option value="PiYG_r">PiYG reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	585 <option value="PRGn_r">PRGn reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	586 <option value="PuOr_r">PuOr reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	587 <option value="PuRd_r">PuRd reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	588 <option value="PuBu_r">PuBu reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	589 <option value="RdBu_r">RdBu reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	590 <option value="RdGy_r">RdGy reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	591 <option value="RdPu_r">RdPu reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	592 <option value="YlGn_r">YlGn reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	593 <option value="PuBuGn_r">PuBuGn reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	594 <option value="RdYlBu_r">RdYlBu reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	595 <option value="RdYlGn_r">RdYlGn reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	596 <option value="YlGnBu_r">YlGnBu reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	597 <option value="YlOrBr_r">YlOrBr reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	598 <option value="YlOrRd_r">YlOrRd reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	599 <option value="gist_gray_r">gist_gray reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	600 <option value="gist_stern_r">gist_stern reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	601 <option value="gist_earth_r">gist_earth reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	602 <option value="gist_yarg_r">gist_yarg reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	603 <option value="gist_ncar_r">gist_ncar reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	604 <option value="gist_rainbow_r">gist_rainbow reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	605 <option value="gist_heat_r">gist_heat reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	606 <option value="gnuplot_r">gnuplot reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	607 <option value="gnuplot2_r">gnuplot2 reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	608 <option value="CMRmap_r">CMRmap reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	609 <option value="bwr_r">bwr reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	610 <option value="hsv_r">hsv reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	611 <option value="brg_r">brg reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	612 <option value="jet_r">jet reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	613 <option value="afmhot_r">afmhot reversed</option>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	614 </param>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	615
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	616 </xml>
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	617
b0050909cf03 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	618 </macros>

Mercurial > repos > bgruening > deeptools_plot_correlation

annotate deepTools_macros.xml @ 1:08b01bdab227 draft