deeptools_plot_profile: deepTools

annotate deepTools_macros.xml @ 22:e6cf706b144b draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit beb75870e99ed8ceca69753bf7de546877b3e2ff

author	bgruening
date	Fri, 12 Aug 2016 05:18:13 -0400
parents	555739cc510f
children	06277c005b1a

rev	line source
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	1 <macros>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	2
506970788461 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">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	4 <conditional name="advancedOpt">
506970788461 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" >
506970788461 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>
506970788461 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>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	8 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	9 <when value="no" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	10 <when value="yes">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	11 <yield/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	12 </when>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	13 </conditional>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	14 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	15
506970788461 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 91515a3e9d14 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':
91515a3e9d14 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
91515a3e9d14 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':
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	20 --extendReads
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	21 #end if
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	22 $advancedOpt.ignoreDuplicates
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	23 $advancedOpt.centerReads
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	24 #if $advancedOpt.minMappingQuality:
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	25 --minMappingQuality '$advancedOpt.minMappingQuality'
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	26 #end if
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	27 #if $advancedOpt.samFlagInclude:
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	28 --samFlagInclude $advancedOpt.samFlagInclude
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	29 #end if
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	30 #if $advancedOpt.samFlagExclude:
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	31 --samFlagExclude $advancedOpt.samFlagExclude
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	32 #end if
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	33 #if $advancedOpt.minFragmentLength:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	34 --minFragmentLength $advancedOpt.minFragmentLength
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	35 #end if
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	36 #if $advancedOpt.maxFragmentLength:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	37 --maxFragmentLength $advancedOpt.maxFragmentLength
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	38 #end if
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	39 </token>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	40
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	41 <token name="@ADVANCED_OPTS_GTF@">
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	42 $advancedOpt.metagene
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	43 #if $advancedOpt.transcriptID:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	44 --transcriptID $advancedOpt.transcriptID
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	45 #end if
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	46 #if $advancedOpt.exonID:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	47 --exonID $advancedOpt.exonID
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	48 #end if
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	49 #if $advancedOpt.transcript_id_designator:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	50 --transcript_id_designator $advancedOpt.transcript_id_designator
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	51 #end if
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	52 </token>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	53
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	54 <xml name="heatmap_options">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	55 <expand macro="zMin_zMax" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	56 <expand macro="colorMap" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	57 <expand macro="plotTitle" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	58 <expand macro="plotNumbers" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	59 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	60
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	61 <token name="@HEATMAP_OPTIONS@">
7 a6d65190c7e5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	62 #if str($plotting_type.zMin) != "":
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	63 --zMin $plotting_type.zMin
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	64 #end if
7 a6d65190c7e5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	65 #if str($plotting_type.zMax) != "":
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	66 --zMax $plotting_type.zMax
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	67 #end if
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	68 --colorMap '$plotting_type.colorMap'
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	69 $plotting_type.plotNumbers
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	70 --plotTitle '$plotting_type.plotTitle'
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	71 </token>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	72
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	73
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	74 <xml name="includeZeros">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	75 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	76 label="Include zeros"
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	77 help="If set, then regions with zero counts for all BAM files are included. The default behavior is to ignore such regions." />
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	78 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	79
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	80 <xml name="zMin_zMax">
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	81 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	82 help="If not specified the value is set automatically."/>
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	83 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	84 help="If not specified the value is set automatically."/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	85 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	86
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	87 <xml name="region_limit_operation">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	88 <param argument="--region" type="text" value=""
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	89 label="Region of the genome to limit the operation to"
19 36947e3103a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	90 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".">
36947e3103a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	91 <sanitizer>
36947e3103a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	92 <valid initial="string.letters,string.digits">
36947e3103a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	93 <add value="\|"/>
36947e3103a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	94 </valid>
36947e3103a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	95 </sanitizer>
36947e3103a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	96 </param>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	97 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	98
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	99 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
22 e6cf706b144b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit beb75870e99ed8ceca69753bf7de546877b3e2ff bgruening parents: 21 diff changeset	100 <token name="@WRAPPER_VERSION@">2.3.3</token>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	101 <xml name="requirements">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	102 <requirements>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	103 <requirement type="package" version="2.7.10">python</requirement>
22 e6cf706b144b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit beb75870e99ed8ceca69753bf7de546877b3e2ff bgruening parents: 21 diff changeset	104 <requirement type="package" version="2.3.3">deepTools</requirement>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	105 <yield />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	106 </requirements>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	107 <expand macro="stdio" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	108 <version_command>@BINARY@ --version</version_command>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	109 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	110
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	111 <xml name="smoothLength">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	112 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	113 label="Smooth values using the following length (in bases)"
4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	114 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	115 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	116
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	117
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	118 <xml name="kmeans_clustering">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	119 <conditional name="used_multiple_regions">
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	120 <param name="used_multiple_regions_options" type="select"
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	121 label="Did you compute the matrix with more than one groups of regions?"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	122 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.">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	123 <option value="yes">Yes, I used multiple groups of regions</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	124 <option value="no">No, I used only one group</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	125 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	126 <when value="no">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	127 <conditional name="clustering">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	128 <param name="clustering_options" type="select" label="Clustering algorithm">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	129 <option value="none">No clustering</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	130 <option value="kmeans">Kmeans clustering</option>
13 d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	131 <option value="hclust">Hierarchical clustering</option>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	132 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	133 <when value="kmeans">
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	134 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	135 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	136 This only works for data that is not grouped, otherwise only the first group will be clustered.
7 a6d65190c7e5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69 bgruening parents: 6 diff changeset	137 If more specific clustering methods are required it is advisable to save the underlying matrix and
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	138 run the clustering using other software."/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	139 </when>
13 d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	140 <when value="hclust">
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	141 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	142 help="WARNING: This option causes the tool to run for a very long time! When this option is
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	143 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	144 This only works for data that is not grouped, otherwise only the first group will be clustered.
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	145 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	146 If more specific clustering methods are required it is advisable to save the underlying matrix and
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	147 run the clustering using other software."/>
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	148 </when>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	149 <when value="none" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	150 </conditional>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	151 </when>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	152 <when value="yes" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	153 </conditional>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	154 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	155
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	156 <token name="@KMEANS_CLUSTERING@">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	157 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	158 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	159 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	160 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	161 #end if
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	162 #end if
13 d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	163 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	164 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	165 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	166 #end if
d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	167 #end if
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	168 #end if
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	169 </token>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	170
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	171 <xml name="samFlags">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	172 <param argument="--samFlagInclude" type="integer" optional="True" value=""
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	173 label="Include reads based on the SAM flag"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	174 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."/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	175 <param argument="--samFlagExclude" type="integer" optional="True" value=""
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	176 label="Exclude reads based on the SAM flag"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	177 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."/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	178 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	179
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	180 <xml name="fragLength">
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	181 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	182 label="Minimum fragment length for inclusion."
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	183 help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	184 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	185 label="Maximum fragment length for inclusion."
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	186 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	187 </xml>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	188
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	189 <xml name="read_processing_options">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	190 <expand macro="extendReads" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	191 <expand macro="ignoreDuplicates" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	192 <expand macro="centerReads" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	193 <expand macro="minMappingQuality" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	194 <expand macro="samFlags" />
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	195 <expand macro="fragLength" />
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	196 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	197
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	198 <xml name="gtf_options">
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	199 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	200 label="Use a metagene model"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	201 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	202 <param argument="--transcriptID" optional="True" value="transcript" type="text"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	203 label="trascript designator"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	204 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	205 <param argument="--exonID" optional="True" value="exon" type="text"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	206 label="exon designator"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	207 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	208 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	209 label="transcriptID key designator"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	210 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	211 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	212 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	213 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	214 </xml>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	215
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	216
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	217 <xml name="plotNumbers">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	218 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	219 label="Plot the correlation value"
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	220 help="If set, then the correlation number is plotted on top of the heatmap."/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	221 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	222
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	223 <xml name="extendReads">
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	224 <conditional name="doExtendCustom">
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	225 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	226 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.
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	227 By default each read mate is extended.
4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	228 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	229 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	230 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
4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	231 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	232 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	233 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	234 <option value="custom">A custom length, which will be applied to ALL reads.</option>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	235 </param>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	236 <when value="no" />
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	237 <when value="yes" />
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	238 <when value="custom">
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	239 <param name="extendReadsValue" type="integer" value="300" min="1"
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	240 label="Extend reads to the given average fragment size"
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	241 help="Extend all reads to this length" />
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	242 </when>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	243 </conditional>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	244 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	245
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	246 <xml name="corMethod">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	247 <param argument="--corMethod" type="select" label="Correlation method">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	248 <option value="spearman" selected="True">Spearman</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	249 <option value="pearson">Pearson</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	250 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	251 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	252
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	253 <xml name="distanceBetweenBins">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	254 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	255 label="Distance between bins"
11 5356d393bb69 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: 9 diff changeset	256 help="By default, multiBamSummary considers consecutive bins of
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	257 the specified 'Bin size'. However, to reduce the
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	258 computation time, a larger distance between bins can
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	259 be given. Larger distances result in fewer bins being
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	260 considered."/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	261 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	262
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	263 <xml name="centerReads">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	264 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	265 label="Center regions with respect to the fragment length"
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	266 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	267 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	268
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	269 <xml name="ignoreDuplicates">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	270 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	271 label="Ignore duplicates"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	272 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." />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	273 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	274
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	275 <xml name="sortUsing">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	276 <param argument="--sortUsing" type="select" label="Method used for sorting"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	277 help="For each row the method is computed.">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	278 <option value="mean" selected="true">mean</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	279 <option value="median">median</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	280 <option value="min">min</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	281 <option value="max">max</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	282 <option value="sum">sum</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	283 <option value="region_length">region length</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	284 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	285 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	286
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	287 <xml name="sortRegions">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	288 <param argument="--sortRegions" type="select" label="Sort regions"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	289 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	290 <option value="no">no ordering</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	291 <option value="descend" selected="true">descending order</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	292 <option value="ascend">ascending order</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	293 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	294 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	295
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	296 <xml name="minMappingQuality">
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	297 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	298 label="Minimum mapping quality"
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	299 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	300 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	301
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	302 <xml name="skipZeros">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	303 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	304 label ="Skip zeros"
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	305 help ="If set, then zero counts that happen for all BAM files given are ignored. This may result in fewer considered regions." />
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	306 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	307
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	308 <xml name="fragmentLength">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	309 <param argument="--fragmentLength" type="integer" value="300" min="1"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	310 label="Fragment length used for the sequencing"
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	311 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	312 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	313
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	314 <xml name="scaleFactor">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	315 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	316 help="When used in combination with --normalizeTo1x or
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	317 --normalizeUsingRPKM, the computed scaling factor will
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	318 be multiplied by the given scale factor." />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	319 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	320
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	321 <xml name="scaleFactors">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	322 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	323 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	324 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	325
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	326 <xml name="stdio">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	327 <stdio>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	328 <exit_code range="1:" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	329 <exit_code range=":-1" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	330 <regex match="Error:" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	331 <regex match="Exception:" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	332 <regex match="EXception:" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	333 <regex match="Traceback" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	334 </stdio>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	335 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	336
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	337 <xml name="pseudocount">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	338 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	339 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	340
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	341 <token name="@REFERENCES@">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	342
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	343 .. class:: infomark
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	344
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	345 For more information on the tools, please visit our `help site`_.
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	346
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	347 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	348
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	349 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	350
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	351 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	352 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	353 .. _help site: https://deeptools.readthedocs.org/
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	354
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	355 </token>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	356 <xml name="citations">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	357 <citations>
19 36947e3103a0 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 18 diff changeset	358 <citation type="doi">10.1093/nar/gkw257</citation>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	359 <yield />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	360 </citations>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	361 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	362
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	363 <xml name="multiple_input_bams">
14 3e2de17147d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 13 diff changeset	364 <param argument="--bamfiles" type="data" format="bam" min="1"
3e2de17147d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 13 diff changeset	365 label="Bam file" multiple="true"
16 a3d4a84b8c47 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c bgruening parents: 14 diff changeset	366 help=""/>
14 3e2de17147d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 13 diff changeset	367 </xml>
3e2de17147d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 13 diff changeset	368
3e2de17147d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 13 diff changeset	369 <xml name="multiple_input_bams_min2">
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	370 <param argument="--bamfiles" type="data" format="bam" min="2"
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	371 label="Bam file" multiple="true"
16 a3d4a84b8c47 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c bgruening parents: 14 diff changeset	372 help=""/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	373 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	374
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	375 <xml name="multiple_input_bigwigs">
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	376 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	377 label="Bigwig file"
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	378 help="A Bigwig file."/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	379 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	380
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	381 <xml name="plotTitle">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	382 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	383 label="Title of the plot"
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	384 help="Title of the plot, to be printed on top of the generated image." />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	385 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	386
13 d2205d523d83 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 12 diff changeset	387
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	388 <token name="@multiple_input_bams@">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	389 <![CDATA[
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	390 #set files=[]
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	391 #set labels=[]
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	392 #for $counter, $bamfile in enumerate($bamfiles):
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	393 ln -s "${bamfile}" "./${counter}.bam" &&
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	394 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	395 #silent $files.append('%s.bam' % $counter)
18 eb83a15755dd planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356 bgruening parents: 16 diff changeset	396 #silent $labels.append("'%s'" % ($bamfile.display_name))
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	397 #end for
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	398 ]]>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	399 </token>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	400
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	401 <token name="@multiple_input_bigwigs@">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	402 <![CDATA[
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	403 #set files=[]
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	404 #set labels=[]
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	405 #for $counter, $bigwig in enumerate($bigwigfiles):
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	406 ln -s "${bigwig}" "${counter}.bw" &&
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	407 #silent $files.append('%s.bw' % $counter)
18 eb83a15755dd planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356 bgruening parents: 16 diff changeset	408 #silent $labels.append("'%s'" % ($bigwig.display_name))
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	409 #end for
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	410 ]]>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	411 </token>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	412
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	413 <xml name="blacklist">
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	414 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	415 label="Blacklisted regions in BED/GTF format"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	416 help="One or more files containing regions to exclude from the analysis" />
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	417 </xml>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	418
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	419 <token name="@blacklist@">
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	420 <![CDATA[
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	421 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	422 #set blfiles=[]
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	423 #for $f in $advancedOpt.blackListFileName:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	424 #silent $blfiles.append("'%s'" % $f)
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	425 #end for
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	426 #if $blfiles != ["'None'"]:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	427 --blackListFileName #echo ' '.join($blfiles)#
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	428 #end if
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	429 #end if
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	430 ]]>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	431 </token>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	432
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	433 <xml name="multiple_bed">
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	434 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	435 label="Regions in BED/GTF format"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	436 help="One or more files containing regions to include in the analysis" />
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	437 </xml>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	438
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	439 <token name="@multiple_bed@">
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	440 <![CDATA[
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	441 #set files=[]
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	442 #set labels=[]
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	443 #for $f in $BED:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	444 #silent $files.append("'%s'" % $f)
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	445 #silent $labels.append("'%s'" % $f.display_name)
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	446 #end for
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	447 #if len($files) > 0:
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	448 --BED #echo ' '.join($files)#
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	449 --regionLabels #echo ' '.join($labels)#
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	450 #end if
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	451 ]]>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	452 </token>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	453
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	454 <xml name="reference_genome_source">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	455 <conditional name="source">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	456 <param name="ref_source" type="select" label="Reference genome">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	457 <option value="cached">locally cached</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	458 <option value="history">in your history</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	459 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	460 <when value="cached">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	461 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	462 <options from_data_table="lastz_seqs">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	463 <filter type="sort_by" column="1" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	464 <validator type="no_options" message="No indexes are available." />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	465 </options>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	466 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	467 </when>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	468 <when value="history">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	469 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	470 </when>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	471 </conditional>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	472 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	473
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	474 <token name="@reference_genome_source@">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	475 #if $source.ref_source=="history":
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	476 --genome $source.input1
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	477 #else:
4 4213153d3b82 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty bgruening parents: 3 diff changeset	478 --genome "$source.input1_2bit.fields.path"
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	479 #end if
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	480 </token>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	481
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	482 <xml name="effectiveGenomeSize">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	483 <conditional name="effectiveGenomeSize">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	484 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	485 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.
2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	486 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	487 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.">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	488 <option value="93260000">ce10 (93260000)</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	489 <option value="121400000">dm3 (121400000)</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	490 <option value="2451960000" selected="true">hg19 (2451960000)</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	491 <option value="2150570000">mm9 (2150570000)</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	492 <option value="specific">user specified</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	493 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	494 <when value="specific">
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	495 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	496 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	497 </when>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	498 <when value="2150570000" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	499 <when value="2451960000" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	500 <when value="121400000" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	501 <when value="93260000" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	502 </conditional>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	503 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	504
1 ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	505 <xml name="skipNAs">
ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	506 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	507 label="Ignore missing data?"
ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	508 help="This parameter determines if non-covered regions
ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	509 (regions without overlapping reads) in a bam/bigWig file
ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	510 should be skipped. The default is to treat those
ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	511 regions as having a value of zero. The decision to
ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	512 skip non-covered regions depends on the interpretation
8 4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	513 of the data. Non-covered regions may represent, for
4339a4d28e97 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7 bgruening parents: 7 diff changeset	514 example, repetitive regions that should be ignored.
1 ba41cc8bb789 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427 bgruening parents: 0 diff changeset	515 (default: False)" />
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	516 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	517
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	518 <xml name="input_save_matrix_values">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	519 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	520 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	521
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	522 <xml name="input_graphic_output_settings">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	523 <conditional name="output" >
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	524 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	525 <option value="no" selected="true">no</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	526 <option value="yes">yes</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	527 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	528 <when value="no" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	529 <when value="yes">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	530 <yield />
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	531 <param name="saveSortedRegions" type="boolean"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	532 label="Save the regions after skipping zeros or min/max threshold values"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	533 help="The order of the regions in the file follows the sorting order selected. This is useful,
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	534 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	535 </when>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	536 </conditional>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	537 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	538
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	539
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	540 <xml name="input_image_file_format">
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	541 <param argument="--outFileFormat" type="select" label="Image file format">
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	542 <option value="png" selected="true">png</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	543 <option value="pdf">pdf</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	544 <option value="svg">svg</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	545 <option value="eps">eps</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	546 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	547 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	548
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	549 <xml name="output_dpi">
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	550 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	551 label="Image dpi" help=""/>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	552 </xml>
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	553
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	554 <xml name="output_image_file_format">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	555 <data format="png" name="outFileName" label="${tool.name} image">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	556 <change_format>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	557 <when input="output.outFileFormat" value="pdf" format="pdf" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	558 <when input="output.outFileFormat" value="svg" format="svg" />
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	559 <when input="output.outFileFormat" value="eps" format="eps" />
3 91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	560 </change_format>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	561 </data>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	562 </xml>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	563
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	564 <xml name="output_image_file_format_not_nested">
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	565 <data format="png" name="outFileName" label="${tool.name} image">
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	566 <change_format>
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	567 <when input="outFileFormat" value="pdf" format="pdf" />
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	568 <when input="outFileFormat" value="svg" format="svg" />
91515a3e9d14 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f bgruening parents: 2 diff changeset	569 <when input="outFileFormat" value="eps" format="eps" />
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	570 </change_format>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	571 </data>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	572 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	573
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	574 <xml name="output_save_matrix_values">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	575 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	576 <filter>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	577 ((
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	578 output['showOutputSettings'] == 'yes' and
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	579 output['saveMatrix'] is True
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	580 ))
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	581 </filter>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	582 </data>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	583 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	584
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	585 <xml name="output_graphic_outputs">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	586 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	587 <filter>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	588 ((
2 2c7ef70dedb7 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829 bgruening parents: 1 diff changeset	589 output['showOutputSettings'] == 'yes' and
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	590 output['saveSortedRegions'] is True
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	591 ))
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	592 </filter>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	593 </data>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	594 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	595
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	596 <xml name="colorMap">
21 555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	597 <param name="colorMap" type="select" label="Color map to use for the heatmap"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	598 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
555739cc510f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 20 diff changeset	599 multiple="true">
0 506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	600 <option value="RdYlBu" selected="true">RdYlBu</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	601 <option value="Accent">Accent</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	602 <option value="Spectral">Spectral</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	603 <option value="Set1">Set1</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	604 <option value="Set2">Set2</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	605 <option value="Set3">Set3</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	606 <option value="Dark2">Dark2</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	607 <option value="Reds">Reds</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	608 <option value="Oranges">Oranges</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	609 <option value="Greens">Greens</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	610 <option value="Blues">Blues</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	611 <option value="Greys">Greys</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	612 <option value="Purples">Purples</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	613 <option value="Paired">Paired</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	614 <option value="Pastel1">Pastel1</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	615 <option value="Pastel2">Pastel2</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	616 <option value="spring">spring</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	617 <option value="summer">summer</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	618 <option value="autumn">autumn</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	619 <option value="winter">winter</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	620 <option value="hot">hot</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	621 <option value="coolwarm">coolwarm</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	622 <option value="cool">cool</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	623 <option value="seismic">seismic</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	624 <option value="terrain">terrain</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	625 <option value="ocean">ocean</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	626 <option value="rainbow">rainbow</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	627 <option value="bone">bone</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	628 <option value="flag">flag</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	629 <option value="prism">prism</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	630 <option value="cubehelix">cubehelix</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	631 <option value="binary">binary</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	632 <option value="pink">pink</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	633 <option value="gray">gray</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	634 <option value="copper">copper</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	635 <option value="BrBG">BrBG</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	636 <option value="BuGn">BuGn</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	637 <option value="BuPu">BuPu</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	638 <option value="GnBu">GnBu</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	639 <option value="OrRd">OrRd</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	640 <option value="PiYG">PiYG</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	641 <option value="PRGn">PRGn</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	642 <option value="PuOr">PuOr</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	643 <option value="PuRd">PuRd</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	644 <option value="PuBu">PuBu</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	645 <option value="RdBu">RdBu</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	646 <option value="RdGy">RdGy</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	647 <option value="RdPu">RdPu</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	648 <option value="YlGn">YlGn</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	649 <option value="PuBuGn">PuBuGn</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	650 <option value="RdYlGn">RdYlGn</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	651 <option value="YlGnBu">YlGnBu</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	652 <option value="YlOrBr">YlOrBr</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	653 <option value="YlOrRd">YlOrRd</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	654 <option value="gist_gray">gist_gray</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	655 <option value="gist_stern">gist_stern</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	656 <option value="gist_earth">gist_earth</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	657 <option value="gist_yarg">gist_yarg</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	658 <option value="gist_ncar">gist_ncar</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	659 <option value="gist_rainbow">gist_rainbow</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	660 <option value="gist_heat">gist_heat</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	661 <option value="gnuplot">gnuplot</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	662 <option value="gnuplot2">gnuplot2</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	663 <option value="CMRmap">CMRmap</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	664 <option value="bwr">bwr</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	665 <option value="hsv">hsv</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	666 <option value="brg">brg</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	667 <option value="jet">jet</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	668 <option value="afmhot">afmhot</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	669 <option value="Accent_r">Accent reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	670 <option value="Spectral_r">Spectral reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	671 <option value="Set1_r">Set1 reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	672 <option value="Set2_r">Set2 reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	673 <option value="Set3_r">Set3 reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	674 <option value="Dark2_r">Dark2 reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	675 <option value="Reds_r">Reds reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	676 <option value="Oranges_r">Oranges reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	677 <option value="Greens_r">Greens reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	678 <option value="Blues_r">Blues reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	679 <option value="Greys_r">Greys reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	680 <option value="Purples_r">Purples reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	681 <option value="Paired_r">Paired reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	682 <option value="Pastel1_r">Pastel1 reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	683 <option value="Pastel2_r">Pastel2 reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	684 <option value="spring_r">spring reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	685 <option value="summer_r">summer reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	686 <option value="autumn_r">autumn reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	687 <option value="winter_r">winter reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	688 <option value="hot_r">hot reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	689 <option value="coolwarm_r">coolwarm reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	690 <option value="cool_r">cool reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	691 <option value="seismic_r">seismic reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	692 <option value="terrain_r">terrain reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	693 <option value="ocean_r">ocean reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	694 <option value="rainbow_r">rainbow reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	695 <option value="bone_r">bone reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	696 <option value="flag_r">flag reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	697 <option value="prism_r">prism reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	698 <option value="cubehelix_r">cubehelix reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	699 <option value="binary_r">binary reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	700 <option value="pink_r">pink reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	701 <option value="gray_r">gray reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	702 <option value="copper_r">copper reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	703 <option value="BrBG_r">BrBG reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	704 <option value="BuGn_r">BuGn reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	705 <option value="BuPu_r">BuPu reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	706 <option value="GnBu_r">GnBu reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	707 <option value="OrRd_r">OrRd reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	708 <option value="PiYG_r">PiYG reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	709 <option value="PRGn_r">PRGn reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	710 <option value="PuOr_r">PuOr reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	711 <option value="PuRd_r">PuRd reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	712 <option value="PuBu_r">PuBu reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	713 <option value="RdBu_r">RdBu reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	714 <option value="RdGy_r">RdGy reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	715 <option value="RdPu_r">RdPu reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	716 <option value="YlGn_r">YlGn reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	717 <option value="PuBuGn_r">PuBuGn reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	718 <option value="RdYlBu_r">RdYlBu reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	719 <option value="RdYlGn_r">RdYlGn reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	720 <option value="YlGnBu_r">YlGnBu reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	721 <option value="YlOrBr_r">YlOrBr reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	722 <option value="YlOrRd_r">YlOrRd reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	723 <option value="gist_gray_r">gist_gray reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	724 <option value="gist_stern_r">gist_stern reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	725 <option value="gist_earth_r">gist_earth reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	726 <option value="gist_yarg_r">gist_yarg reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	727 <option value="gist_ncar_r">gist_ncar reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	728 <option value="gist_rainbow_r">gist_rainbow reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	729 <option value="gist_heat_r">gist_heat reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	730 <option value="gnuplot_r">gnuplot reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	731 <option value="gnuplot2_r">gnuplot2 reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	732 <option value="CMRmap_r">CMRmap reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	733 <option value="bwr_r">bwr reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	734 <option value="hsv_r">hsv reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	735 <option value="brg_r">brg reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	736 <option value="jet_r">jet reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	737 <option value="afmhot_r">afmhot reversed</option>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	738 </param>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	739
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	740 </xml>
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	741
506970788461 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty bgruening parents: diff changeset	742 </macros>

Mercurial > repos > bgruening > deeptools_plot_profile

annotate deepTools_macros.xml @ 22:e6cf706b144b draft