deeptools_compute_matrix: deepTools

annotate deepTools_macros.xml @ 7:021729469baf draft

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

author	bgruening
date	Wed, 23 Dec 2015 07:34:34 -0500
parents	451e73bf38fe
children	e3f4303309cc

rev	line source
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	1 <macros>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	2
f1db8b6a8743 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">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	4 <conditional name="advancedOpt">
f1db8b6a8743 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" >
f1db8b6a8743 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>
f1db8b6a8743 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>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	8 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	9 <when value="no" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	10 <when value="yes">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	11 <yield/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	12 </when>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	13 </conditional>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	14 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	15
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	20 --extendReads
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	21 #end if
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	23 $advancedOpt.centerReads
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	26 #end if
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	29 #end if
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	32 #end if
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	33 </token>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	34
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	35 <xml name="heatmap_options">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	36 <expand macro="zMin_zMax" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	37 <expand macro="colorMap" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	38 <expand macro="plotTitle" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	39 <expand macro="plotNumbers" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	40 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	41
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	42 <token name="@HEATMAP_OPTIONS@">
7 021729469baf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	43 #if str($plotting_type.zMin) != "":
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	44 --zMin $plotting_type.zMin
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	45 #end if
7 021729469baf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	46 #if str($plotting_type.zMax) != "":
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	47 --zMax $plotting_type.zMax
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	48 #end if
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	49 --colorMap '$plotting_type.colorMap'
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	50 $plotting_type.plotNumbers
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	51 --plotTitle '$plotting_type.plotTitle'
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	52 </token>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	53
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	54
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	55 <xml name="includeZeros">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	57 label="Include zeros"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	58 help="If set, then regions with zero counts for all BAM files given are included. The default behavior is to ignore those cases." />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	59 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	60
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	61 <xml name="zMin_zMax">
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	63 help="If not specified the value is set automatically."/>
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	65 help="If not specified the value is set automatically."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	66 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	67
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	68 <xml name="region_limit_operation">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	69 <param argument="--region" type="text" value=""
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	70 label="Region of the genome to limit the operation to"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	71 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	72 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	73
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
1 de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	75 <token name="@WRAPPER_VERSION@">2.0.0</token>
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	76 <xml name="requirements">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	77 <requirements>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	78 <requirement type="package" version="2.7.10">python</requirement>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	79 <requirement type="binary">@BINARY@</requirement>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	80 <requirement type="package" version="2.0">deepTools</requirement>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	81 <yield />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	82 </requirements>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	83 <expand macro="stdio" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	84 <version_command>@BINARY@ --version</version_command>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	85 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	86
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	87 <xml name="smoothLength">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	88 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	89 label="Smooth values using the following length (in bp)"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	90 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	91 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	92
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	93
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	94 <xml name="kmeans_clustering">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	95 <conditional name="used_multiple_regions">
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	96 <param name="used_multiple_regions_options" type="select"
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	97 label="Did you compute the matrix with more than one groups of regions?"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	98 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	99 <option value="yes">Yes, I used multiple groups of regions</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	100 <option value="no">No, I used only one group</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	101 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	102 <when value="no">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	103 <conditional name="clustering">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	104 <param name="clustering_options" type="select" label="Clustering algorithm">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	105 <option value="none">No clustering</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	106 <option value="kmeans">Kmeans clustering</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	107 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	108 <when value="kmeans">
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	109 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
7 021729469baf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	110 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm.
021729469baf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	111 Only works for data that is not grouped, otherwise only the first group will be clustered.
021729469baf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	112 If more specific clustering methods are required it is advisable to save the underlying matrix and
021729469baf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	113 run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault)
021729469baf planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	114 if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/>
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	115 </when>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	116 <when value="none" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	117 </conditional>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	118 </when>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	119 <when value="yes" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	120 </conditional>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	121 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	122
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	123 <token name="@KMEANS_CLUSTERING@">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	124 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	125 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	126 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	127 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	128 #end if
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	129 #end if
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	130 #end if
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	131 </token>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	132
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	133 <xml name="samFlags">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	134 <param argument="--samFlagInclude" type="integer" optional="True" value=""
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	135 label="Include reads based on the SAM flag"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	136 help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	137 <param argument="--samFlagExclude" type="integer" optional="True" value=""
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	138 label="Exclude reads based on the SAM flag"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	139 help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	140 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	141
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	142 <xml name="read_processing_options">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	143 <expand macro="extendReads" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	144 <expand macro="ignoreDuplicates" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	145 <expand macro="centerReads" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	146 <expand macro="minMappingQuality" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	147 <expand macro="samFlags" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	148 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	149
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	150 <xml name="plotNumbers">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	151 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	152 label="Plot the correlation value"
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	153 help="If set, then the correlation number is plotted on top of the heatmap."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	154 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	155
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	156 <xml name="extendReads">
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	157 <conditional name="doExtendCustom">
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	158 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	159 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	160 By default each read mate is extended.
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	161 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	162 Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	163 Reads are only extended if --extendReads is set to a value greater than the read length. NOTE: For spliced-read data, this option is not
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	164 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	165 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	166 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	167 <option value="custom">A custom length, which will be applied to ALL reads.</option>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	168 </param>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	169 <when value="no" />
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	170 <when value="yes" />
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	171 <when value="custom">
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	172 <param name="extendReadsValue" type="integer" value="300" min="1"
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	173 label="Extend reads to the given average fragment size"
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	174 help="Extend all reads to this length" />
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	175 </when>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	176 </conditional>
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	177 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	178
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	179 <xml name="corMethod">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	180 <param argument="--corMethod" type="select" label="Correlation method">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	181 <option value="spearman" selected="True">Spearman</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	182 <option value="pearson">Pearson</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	183 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	184 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	185
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	186 <xml name="distanceBetweenBins">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	187 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	188 label="Distance between bins"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	189 help="By default, bamCorrelate considers consecutive bins of
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	190 the specified 'Bin size'. However, to reduce the
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	191 computation time, a larger distance between bins can
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	192 by given. Larger distances result in less bins being
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	193 considered."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	194 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	195
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	196 <xml name="centerReads">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	197 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	198 label="Center regions with respect to the fragment length"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	199 help="For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. "/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	200 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	201
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	202 <xml name="ignoreDuplicates">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	203 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	204 label="Ignore duplicates"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	205 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	206 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	207
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	208 <xml name="sortUsing">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	209 <param argument="--sortUsing" type="select" label="Method used for sorting"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	210 help="For each row the method is computed.">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	211 <option value="mean" selected="true">mean</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	212 <option value="median">median</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	213 <option value="min">min</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	214 <option value="max">max</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	215 <option value="sum">sum</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	216 <option value="region_length">region length</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	217 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	218 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	219
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	220 <xml name="sortRegions">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	221 <param argument="--sortRegions" type="select" label="Sort regions"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	222 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	223 <option value="no">no ordering</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	224 <option value="descend" selected="true">descending order</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	225 <option value="ascend">ascending order</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	226 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	227 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	228
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	229 <xml name="minMappingQuality">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	230 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	231 label="Minimum mapping quality"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	232 help= "If set, only reads that have a mapping quality score higher than the given value are considered. Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	233 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	234
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	235 <xml name="skipZeros">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	236 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	237 label ="Skip zeros"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	238 help ="If set, then zero counts that happen for all BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	239 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	240
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	241 <xml name="fragmentLength">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	242 <param argument="--fragmentLength" type="integer" value="300" min="1"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	243 label="Fragment length used for the sequencing"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	244 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	245 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	246
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	247 <xml name="scaleFactor">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	248 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	249 help="When used in combination with --normalizeTo1x or
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	250 --normalizeUsingRPKM, the computed scaling factor will
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	251 be multiplied by the given scale factor." />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	252 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	253
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	254 <xml name="scaleFactors">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	255 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	256 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	257 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	258
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	259 <xml name="stdio">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	260 <stdio>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	261 <exit_code range="1:" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	262 <exit_code range=":-1" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	263 <regex match="Error:" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	264 <regex match="Exception:" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	265 <regex match="EXception:" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	266 <regex match="Traceback" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	267 </stdio>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	268 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	269
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	270 <xml name="pseudocount">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	271 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	272 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	273
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	274 <token name="@REFERENCES@">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	275
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	276 .. class:: infomark
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	277
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	278 For more information on the tools, please visit our `help site`_.
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	279
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	280 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	281
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	282 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	283
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	284 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	285 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	286 .. _help site: https://deeptools.readthedocs.org/
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	287
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	288 </token>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	289 <xml name="citations">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	290 <citations>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	291 <citation type="doi">10.1093/nar/gku365</citation>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	292 <yield />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	293 </citations>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	294 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	295
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	296 <xml name="multiple_input_bams">
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	297 <param argument="--bamfiles" type="data" format="bam" min="2"
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	298 label="Bam file" multiple="true"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	299 help="The BAM file must be sorted."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	300 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	301
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	302 <xml name="multiple_input_bigwigs">
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	303 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	304 label="Bigwig file"
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	305 help="The Bigwig file must be sorted."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	306 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	307
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	308 <xml name="plotTitle">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	309 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	310 label="Title of the plot"
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	311 help="Title of the plot, to be printed on top of the generated image." />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	312 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	313
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	314 <token name="@multiple_input_bams@">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	315 <![CDATA[
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	316 #set files=[]
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	317 #set labels=[]
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	318 #for $counter, $bamfile in enumerate($bamfiles):
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	319 ln -s "${bamfile}" "./${counter}.bam" &&
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	320 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	321 #silent $files.append('%s.bam' % $counter)
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	322 #silent $labels.append('%s' % ($bamfile.display_name))
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	323 #end for
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	324 ]]>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	325 </token>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	326
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	327 <token name="@multiple_input_bigwigs@">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	328 <![CDATA[
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	329 #set files=[]
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	330 #set labels=[]
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	331 #for $counter, $bigwig in enumerate($bigwigfiles):
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	332 ln -s "${bigwig}" "${counter}.bw" &&
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	333 #silent $files.append('%s.bw' % $counter)
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	334 #silent $labels.append('%s' % ($bigwig.display_name))
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	335 #end for
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	336 ]]>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	337 </token>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	338
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	339 <xml name="reference_genome_source">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	340 <conditional name="source">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	341 <param name="ref_source" type="select" label="Reference genome">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	342 <option value="cached">locally cached</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	343 <option value="history">in your history</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	344 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	345 <when value="cached">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	346 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	347 <options from_data_table="lastz_seqs">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	348 <filter type="sort_by" column="1" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	349 <validator type="no_options" message="No indexes are available." />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	350 </options>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	351 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	352 </when>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	353 <when value="history">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	354 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	355 </when>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	356 </conditional>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	357 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	358
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	359 <token name="@reference_genome_source@">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	360 #if $source.ref_source=="history":
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	361 --genome $source.input1
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	362 #else:
4 28b07293f1ab planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: 3 diff changeset	363 --genome "$source.input1_2bit.fields.path"
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	364 #end if
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	365 </token>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	366
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	367 <xml name="effectiveGenomeSize">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	368 <conditional name="effectiveGenomeSize">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	369 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	370 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	371 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	372 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	373 <option value="93260000">ce10 (93260000)</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	374 <option value="121400000">dm3 (121400000)</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	375 <option value="2451960000" selected="true">hg19 (2451960000)</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	376 <option value="2150570000">mm9 (2150570000)</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	377 <option value="specific">user specified</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	378 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	379 <when value="specific">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	380 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	381 </when>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	382 <when value="2150570000" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	383 <when value="2451960000" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	384 <when value="121400000" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	385 <when value="93260000" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	386 </conditional>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	387 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	388
1 de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	389 <xml name="skipNAs">
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	390 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	391 label="Ignore missing data?"
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	392 help="This parameter determines if non-covered regions
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	393 (regions without overlapping reads) in a bam/bigWig file
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	394 should be skipped. The default is to treat those
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	395 regions as having a value of zero. The decision to
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	396 skip non-covered regions depends on the interpretation
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	397 of the data. Non-covered regions may represent for
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	398 example repetitive regions that want to be skipped.
de51aa03c9b9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	399 (default: False)" />
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	400 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	401
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	402 <xml name="input_save_matrix_values">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	403 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	404 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	405
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	406 <xml name="input_graphic_output_settings">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	407 <conditional name="output" >
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	408 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	409 <option value="no" selected="true">no</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	410 <option value="yes">yes</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	411 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	412 <when value="no" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	413 <when value="yes">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	414 <yield />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	415 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	416 </when>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	417 </conditional>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	418 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	419
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	420
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	421 <xml name="input_image_file_format">
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	422 <param argument="--outFileFormat" type="select" label="Image file format">
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	423 <option value="png" selected="true">png</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	424 <option value="pdf">pdf</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	425 <option value="svg">svg</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	426 <option value="eps">eps</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	427 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	428 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	429
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	430 <xml name="output_image_file_format">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	431 <data format="png" name="outFileName" label="${tool.name} image">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	432 <change_format>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	433 <when input="output.outFileFormat" value="pdf" format="pdf" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	434 <when input="output.outFileFormat" value="svg" format="svg" />
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	435 <when input="output.outFileFormat" value="eps" format="eps" />
3 2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	436 </change_format>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	437 </data>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	438 </xml>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	439
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	440 <xml name="output_image_file_format_not_nested">
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	441 <data format="png" name="outFileName" label="${tool.name} image">
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	442 <change_format>
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	443 <when input="outFileFormat" value="pdf" format="pdf" />
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	444 <when input="outFileFormat" value="svg" format="svg" />
2f2dd609644f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	445 <when input="outFileFormat" value="eps" format="eps" />
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	446 </change_format>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	447 </data>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	448 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	449
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	450 <xml name="output_save_matrix_values">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	451 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	452 <filter>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	453 ((
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	454 output['showOutputSettings'] == 'yes' and
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	455 output['saveMatrix'] is True
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	456 ))
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	457 </filter>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	458 </data>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	459 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	460
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	461 <xml name="output_graphic_outputs">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	462 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	463 <filter>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	464 ((
2 fb65748c2594 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	465 output['showOutputSettings'] == 'yes' and
0 f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	466 output['saveSortedRegions'] is True
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	467 ))
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	468 </filter>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	469 </data>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	470 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	471
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	472 <xml name="colorMap">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	473 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	474 <option value="RdYlBu" selected="true">RdYlBu</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	475 <option value="Accent">Accent</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	476 <option value="Spectral">Spectral</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	477 <option value="Set1">Set1</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	478 <option value="Set2">Set2</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	479 <option value="Set3">Set3</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	480 <option value="Dark2">Dark2</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	481 <option value="Reds">Reds</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	482 <option value="Oranges">Oranges</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	483 <option value="Greens">Greens</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	484 <option value="Blues">Blues</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	485 <option value="Greys">Greys</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	486 <option value="Purples">Purples</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	487 <option value="Paired">Paired</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	488 <option value="Pastel1">Pastel1</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	489 <option value="Pastel2">Pastel2</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	490 <option value="spring">spring</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	491 <option value="summer">summer</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	492 <option value="autumn">autumn</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	493 <option value="winter">winter</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	494 <option value="hot">hot</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	495 <option value="coolwarm">coolwarm</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	496 <option value="cool">cool</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	497 <option value="seismic">seismic</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	498 <option value="terrain">terrain</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	499 <option value="ocean">ocean</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	500 <option value="rainbow">rainbow</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	501 <option value="bone">bone</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	502 <option value="flag">flag</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	503 <option value="prism">prism</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	504 <option value="cubehelix">cubehelix</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	505 <option value="binary">binary</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	506 <option value="pink">pink</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	507 <option value="gray">gray</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	508 <option value="copper">copper</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	509 <option value="BrBG">BrBG</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	510 <option value="BuGn">BuGn</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	511 <option value="BuPu">BuPu</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	512 <option value="GnBu">GnBu</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	513 <option value="OrRd">OrRd</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	514 <option value="PiYG">PiYG</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	515 <option value="PRGn">PRGn</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	516 <option value="PuOr">PuOr</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	517 <option value="PuRd">PuRd</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	518 <option value="PuBu">PuBu</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	519 <option value="RdBu">RdBu</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	520 <option value="RdGy">RdGy</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	521 <option value="RdPu">RdPu</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	522 <option value="YlGn">YlGn</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	523 <option value="PuBuGn">PuBuGn</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	524 <option value="RdYlGn">RdYlGn</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	525 <option value="YlGnBu">YlGnBu</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	526 <option value="YlOrBr">YlOrBr</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	527 <option value="YlOrRd">YlOrRd</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	528 <option value="gist_gray">gist_gray</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	529 <option value="gist_stern">gist_stern</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	530 <option value="gist_earth">gist_earth</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	531 <option value="gist_yarg">gist_yarg</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	532 <option value="gist_ncar">gist_ncar</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	533 <option value="gist_rainbow">gist_rainbow</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	534 <option value="gist_heat">gist_heat</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	535 <option value="gnuplot">gnuplot</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	536 <option value="gnuplot2">gnuplot2</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	537 <option value="CMRmap">CMRmap</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	538 <option value="bwr">bwr</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	539 <option value="hsv">hsv</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	540 <option value="brg">brg</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	541 <option value="jet">jet</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	542 <option value="afmhot">afmhot</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	543 <option value="Accent_r">Accent reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	544 <option value="Spectral_r">Spectral reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	545 <option value="Set1_r">Set1 reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	546 <option value="Set2_r">Set2 reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	547 <option value="Set3_r">Set3 reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	548 <option value="Dark2_r">Dark2 reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	549 <option value="Reds_r">Reds reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	550 <option value="Oranges_r">Oranges reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	551 <option value="Greens_r">Greens reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	552 <option value="Blues_r">Blues reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	553 <option value="Greys_r">Greys reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	554 <option value="Purples_r">Purples reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	555 <option value="Paired_r">Paired reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	556 <option value="Pastel1_r">Pastel1 reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	557 <option value="Pastel2_r">Pastel2 reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	558 <option value="spring_r">spring reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	559 <option value="summer_r">summer reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	560 <option value="autumn_r">autumn reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	561 <option value="winter_r">winter reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	562 <option value="hot_r">hot reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	563 <option value="coolwarm_r">coolwarm reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	564 <option value="cool_r">cool reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	565 <option value="seismic_r">seismic reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	566 <option value="terrain_r">terrain reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	567 <option value="ocean_r">ocean reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	568 <option value="rainbow_r">rainbow reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	569 <option value="bone_r">bone reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	570 <option value="flag_r">flag reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	571 <option value="prism_r">prism reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	572 <option value="cubehelix_r">cubehelix reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	573 <option value="binary_r">binary reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	574 <option value="pink_r">pink reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	575 <option value="gray_r">gray reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	576 <option value="copper_r">copper reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	577 <option value="BrBG_r">BrBG reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	578 <option value="BuGn_r">BuGn reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	579 <option value="BuPu_r">BuPu reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	580 <option value="GnBu_r">GnBu reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	581 <option value="OrRd_r">OrRd reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	582 <option value="PiYG_r">PiYG reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	583 <option value="PRGn_r">PRGn reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	584 <option value="PuOr_r">PuOr reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	585 <option value="PuRd_r">PuRd reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	586 <option value="PuBu_r">PuBu reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	587 <option value="RdBu_r">RdBu reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	588 <option value="RdGy_r">RdGy reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	589 <option value="RdPu_r">RdPu reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	590 <option value="YlGn_r">YlGn reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	591 <option value="PuBuGn_r">PuBuGn reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	592 <option value="RdYlBu_r">RdYlBu reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	593 <option value="RdYlGn_r">RdYlGn reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	594 <option value="YlGnBu_r">YlGnBu reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	595 <option value="YlOrBr_r">YlOrBr reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	596 <option value="YlOrRd_r">YlOrRd reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	597 <option value="gist_gray_r">gist_gray reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	598 <option value="gist_stern_r">gist_stern reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	599 <option value="gist_earth_r">gist_earth reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	600 <option value="gist_yarg_r">gist_yarg reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	601 <option value="gist_ncar_r">gist_ncar reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	602 <option value="gist_rainbow_r">gist_rainbow reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	603 <option value="gist_heat_r">gist_heat reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	604 <option value="gnuplot_r">gnuplot reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	605 <option value="gnuplot2_r">gnuplot2 reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	606 <option value="CMRmap_r">CMRmap reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	607 <option value="bwr_r">bwr reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	608 <option value="hsv_r">hsv reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	609 <option value="brg_r">brg reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	610 <option value="jet_r">jet reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	611 <option value="afmhot_r">afmhot reversed</option>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	612 </param>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	613
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	614 </xml>
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	615
f1db8b6a8743 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	616 </macros>

Mercurial > repos > bgruening > deeptools_compute_matrix

annotate deepTools_macros.xml @ 7:021729469baf draft