deeptools_multi_bigwig_summary: deepTools

annotate deepTools_macros.xml @ 18:b72c892aefef draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289

author	bgruening
date	Fri, 31 Mar 2017 08:06:35 -0400
parents	b484160969e9
children	660103debaf6

rev	line source
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	1 <macros>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	2
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	4 <token name="@WRAPPER_VERSION@">2.5.0</token>
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	5 <xml name="requirements">
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	6 <requirements>
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	7 <requirement type="package" version="2.7.10">python</requirement>
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	8 <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	9 <yield />
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	10 </requirements>
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	11 <expand macro="stdio" />
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	12 <version_command>@BINARY@ --version</version_command>
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	13 </xml>
b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	14
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	15 <xml name="advancedOpt_scaffold">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	16 <conditional name="advancedOpt">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	17 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	18 <option value="no" selected="true">no</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	19 <option value="yes">yes</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	20 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	21 <when value="no" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	22 <when value="yes">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	23 <yield/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	24 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	25 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	26 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	27
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	28 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	29 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	30 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	31 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	32 --extendReads
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	33 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	34 $advancedOpt.ignoreDuplicates
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	35 $advancedOpt.centerReads
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	36 #if $advancedOpt.minMappingQuality:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	37 --minMappingQuality '$advancedOpt.minMappingQuality'
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	38 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	39 #if $advancedOpt.samFlagInclude:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	40 --samFlagInclude $advancedOpt.samFlagInclude
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	41 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	42 #if $advancedOpt.samFlagExclude:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	43 --samFlagExclude $advancedOpt.samFlagExclude
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	44 #end if
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	45 #if $advancedOpt.minFragmentLength:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	46 --minFragmentLength $advancedOpt.minFragmentLength
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	47 #end if
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	48 #if $advancedOpt.maxFragmentLength:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	49 --maxFragmentLength $advancedOpt.maxFragmentLength
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	50 #end if
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	51 </token>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	52
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	53 <token name="@ADVANCED_OPTS_GTF@">
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	54 $advancedOpt.metagene
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	55 #if $advancedOpt.transcriptID:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	56 --transcriptID $advancedOpt.transcriptID
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	57 #end if
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	58 #if $advancedOpt.exonID:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	59 --exonID $advancedOpt.exonID
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	60 #end if
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	61 #if $advancedOpt.transcript_id_designator:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	62 --transcript_id_designator $advancedOpt.transcript_id_designator
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	63 #end if
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	64 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	65
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	66 <xml name="heatmap_options">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	67 <expand macro="zMin_zMax" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	68 <expand macro="colorMap" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	69 <expand macro="plotTitle" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	70 <expand macro="plotNumbers" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	71 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	72
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	73 <token name="@HEATMAP_OPTIONS@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	74 #if str($plotting_type.zMin) != "":
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	75 --zMin $plotting_type.zMin
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	76 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	77 #if str($plotting_type.zMax) != "":
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	78 --zMax $plotting_type.zMax
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	79 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	80 --colorMap '$plotting_type.colorMap'
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	81 $plotting_type.plotNumbers
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	82 --plotTitle '$plotting_type.plotTitle'
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	83 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	84
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	85
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	86 <xml name="includeZeros">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	87 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	88 label="Include zeros"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	89 help="If set, then regions with zero counts for all BAM files are included. The default behavior is to ignore such regions." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	90 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	91
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	92 <xml name="zMin_zMax">
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	93 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	94 help="If not specified the value is set automatically."/>
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	95 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	96 help="If not specified the value is set automatically."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	97 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	98
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	99 <xml name="region_limit_operation">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	100 <param argument="--region" type="text" value=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	101 label="Region of the genome to limit the operation to"
10 dd46b5d1882c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	102 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".">
dd46b5d1882c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	103 <sanitizer>
dd46b5d1882c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	104 <valid initial="string.letters,string.digits">
dd46b5d1882c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	105 <add value="\|"/>
14 7414b8b48dae planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 13 diff changeset	106 <add value=":"/>
10 dd46b5d1882c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	107 </valid>
dd46b5d1882c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	108 </sanitizer>
dd46b5d1882c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	109 </param>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	110 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	111
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	112 <xml name="smoothLength">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	114 label="Smooth values using the following length (in bases)"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	115 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	116 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	117
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	118
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	119 <xml name="kmeans_clustering">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	120 <conditional name="used_multiple_regions">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	121 <param name="used_multiple_regions_options" type="select"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	122 label="Did you compute the matrix with more than one groups of regions?"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	123 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.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	124 <option value="yes">Yes, I used multiple groups of regions</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	125 <option value="no">No, I used only one group</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	126 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	127 <when value="no">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	128 <conditional name="clustering">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	129 <param name="clustering_options" type="select" label="Clustering algorithm">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	130 <option value="none">No clustering</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	131 <option value="kmeans">Kmeans clustering</option>
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	132 <option value="hclust">Hierarchical clustering</option>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	133 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	134 <when value="kmeans">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	135 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	136 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	137 This only works for data that is not grouped, otherwise only the first group will be clustered.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	138 If more specific clustering methods are required it is advisable to save the underlying matrix and
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	139 run the clustering using other software."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	140 </when>
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	141 <when value="hclust">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	142 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	143 help="WARNING: This option causes the tool to run for a very long time! When this option is
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	144 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	145 This only works for data that is not grouped, otherwise only the first group will be clustered.
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	146 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	147 If more specific clustering methods are required it is advisable to save the underlying matrix and
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	148 run the clustering using other software."/>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	149 </when>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	150 <when value="none" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	151 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	152 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	153 <when value="yes" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	154 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	155 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	156
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	157 <token name="@KMEANS_CLUSTERING@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	158 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	159 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	160 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	161 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	162 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	163 #end if
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	164 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	165 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	166 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	167 #end if
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	168 #end if
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	169 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	170 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	171
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	172 <xml name="samFlags">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	173 <param argument="--samFlagInclude" type="integer" optional="True" value=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	174 label="Include reads based on the SAM flag"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	175 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	176 <param argument="--samFlagExclude" type="integer" optional="True" value=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	177 label="Exclude reads based on the SAM flag"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	178 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	179 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	180
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	181 <xml name="fragLength">
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	183 label="Minimum fragment length for inclusion."
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	184 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	186 label="Maximum fragment length for inclusion."
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	187 help="A value of 0 (the default) is equivalent to no maximum." />
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	188 </xml>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	189
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	190 <xml name="read_processing_options">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	191 <expand macro="extendReads" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	192 <expand macro="ignoreDuplicates" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	193 <expand macro="centerReads" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	194 <expand macro="minMappingQuality" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	195 <expand macro="samFlags" />
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	196 <expand macro="fragLength" />
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	197 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	198
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	199 <xml name="gtf_options">
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	200 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	201 label="Use a metagene model"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	202 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." />
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	203 <param argument="--transcriptID" optional="True" value="transcript" type="text"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	204 label="trascript designator"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	205 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" />
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	206 <param argument="--exonID" optional="True" value="exon" type="text"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	207 label="exon designator"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	208 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" />
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	209 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	210 label="transcriptID key designator"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	211 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	212 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	213 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	214 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	215 </xml>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	216
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	217
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	218 <xml name="plotNumbers">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	219 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	220 label="Plot the correlation value"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	221 help="If set, then the correlation number is plotted on top of the heatmap."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	222 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	223
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	224 <xml name="extendReads">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	225 <conditional name="doExtendCustom">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	226 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	227 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.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	228 By default each read mate is extended.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	229 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	230 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	231 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
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	232 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	233 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	234 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	235 <option value="custom">A custom length, which will be applied to ALL reads.</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	236 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	237 <when value="no" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	238 <when value="yes" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	239 <when value="custom">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	240 <param name="extendReadsValue" type="integer" value="300" min="1"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	241 label="Extend reads to the given average fragment size"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	242 help="Extend all reads to this length" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	243 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	244 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	245 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	246
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	247 <xml name="corMethod">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	248 <param argument="--corMethod" type="select" label="Correlation method">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	249 <option value="spearman" selected="True">Spearman</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	250 <option value="pearson">Pearson</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	251 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	252 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	253
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	254 <xml name="distanceBetweenBins">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	255 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	256 label="Distance between bins"
2 f297f04e34d3 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee bgruening parents: 0 diff changeset	257 help="By default, multiBamSummary considers consecutive bins of
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	258 the specified 'Bin size'. However, to reduce the
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	259 computation time, a larger distance between bins can
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	260 be given. Larger distances result in fewer bins being
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	261 considered."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	262 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	263
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	264 <xml name="centerReads">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	265 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	266 label="Center regions with respect to the fragment length"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	267 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	268 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	269
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	270 <xml name="ignoreDuplicates">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	271 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	272 label="Ignore duplicates"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	273 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." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	274 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	275
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	276 <xml name="sortUsing">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	277 <param argument="--sortUsing" type="select" label="Method used for sorting"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	278 help="For each row the method is computed.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	279 <option value="mean" selected="true">mean</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	280 <option value="median">median</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	281 <option value="min">min</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	282 <option value="max">max</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	283 <option value="sum">sum</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	284 <option value="region_length">region length</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	285 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	286 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	287
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	288 <xml name="sortRegionsComputeMatrix">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	289 <param argument="--sortRegions" type="select" label="Sort regions"
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	290 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	291 <option value="no">no ordering</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	292 <option value="keep" selected="true">maintain the same ordering as the input files</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	293 <option value="descend">descending order</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	294 <option value="ascend">ascending order</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	295 </param>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	296 </xml>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	297
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	298 <xml name="sortRegions">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	299 <param argument="--sortRegions" type="select" label="Sort regions"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	300 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	301 <option value="no">no ordering</option>
17 b484160969e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 16 diff changeset	302 <option value="descend" selected="true">descending order</option>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	303 <option value="ascend">ascending order</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	304 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	305 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	306
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	307 <xml name="minMappingQuality">
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	308 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	309 label="Minimum mapping quality"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	310 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	311 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	312
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	313 <xml name="skipZeros">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	314 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	315 label ="Skip zeros"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	316 help ="If set, then zero counts that happen for all BAM files given are ignored. This may result in fewer considered regions." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	317 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	318
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	319 <xml name="fragmentLength">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	320 <param argument="--fragmentLength" type="integer" value="300" min="1"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	321 label="Fragment length used for the sequencing"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	322 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."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	323 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	324
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	325 <xml name="scaleFactor">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	326 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	327 help="The computed scaling factor will be multiplied by this (default 1)." />
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	328 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	329
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	330 <xml name="scaleFactors">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	331 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	332 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	333 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	334
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	335 <xml name="stdio">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	336 <stdio>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	337 <exit_code range="1:" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	338 <exit_code range=":-1" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	339 <regex match="Error:" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	340 <regex match="Exception:" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	341 <regex match="EXception:" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	342 <regex match="Traceback" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	343 </stdio>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	344 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	345
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	346 <xml name="pseudocount">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	347 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	348 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	349
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	350 <token name="@REFERENCES@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	351
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	352 .. class:: infomark
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	353
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	354 For more information on the tools, please visit our `help site`_.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	355
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	356 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	357
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	358 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	359
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	360 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	361 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	362 .. _help site: https://deeptools.readthedocs.org/
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	363
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	364 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	365 <xml name="citations">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	366 <citations>
10 dd46b5d1882c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 9 diff changeset	367 <citation type="doi">10.1093/nar/gkw257</citation>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	368 <yield />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	369 </citations>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	370 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	371
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	372 <xml name="multiple_input_bams">
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	373 <conditional name="multibam_conditional">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	374 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	375 <option value="No" selected="true">No</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	376 <option value="Yes">Yes</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	377 </param>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	378 <when value="No">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	379 <param argument="--bamfiles" type="data" format="bam" min="1"
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	380 label="Bam file" multiple="true"
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	381 help=""/>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	382 </when>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	383 <when value="Yes">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	384 <repeat name="multibam_repeats" min="1" title="BAM Files">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	385 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	386 </repeat>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	387 </when>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	388 </conditional>
5 5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	389 </xml>
5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	390
5cfa07c31ce4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 4 diff changeset	391 <xml name="multiple_input_bams_min2">
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	392 <conditional name="multibam_conditional">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	393 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	394 is vital to you, select Yes below.">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	395 <option value="No" selected="true">No</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	396 <option value="Yes">Yes</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	397 </param>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	398 <when value="No">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	399 <param argument="--bamfiles" type="data" format="bam" min="2"
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	400 label="Bam file" multiple="true"
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	401 help=""/>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	402 </when>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	403 <when value="Yes">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	404 <repeat name="multibam_repeats" min="2" title="BAM Files">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	405 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	406 </repeat>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	407 </when>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	408 </conditional>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	409 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	410
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	411 <xml name="multiple_input_bigwigs">
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	412 <conditional name="multibigwig_conditional">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	413 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	414 is vital to you, select Yes below.">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	415 <option value="No" selected="true">No</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	416 <option value="Yes">Yes</option>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	417 </param>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	418 <when value="No">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	419 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	420 label="Bigwig file"
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	421 help="A Bigwig file."/>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	422 </when>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	423 <when value="Yes">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	424 <repeat name="multibigwig_repeats" min="2" title="BigWig files">
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	425 <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	426 </repeat>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	427 </when>
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	428 </conditional>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	429 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	430
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	431 <xml name="plotTitle">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	432 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	433 label="Title of the plot"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	434 help="Title of the plot, to be printed on top of the generated image." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	435 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	436
4 263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11 bgruening parents: 3 diff changeset	437
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	438 <token name="@multiple_input_bams@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	439 <![CDATA[
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	440 #set files=[]
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	441 #set labels=[]
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	442 #import re
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	443 #if $multibam_conditional.orderMatters == "No":
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	444 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	445 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	446 ln -s "${bamfile}" "./${counter}.bam" &&
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	448 #silent $files.append('%s.bam' % $counter)
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	449 #silent $labels.append("'%s'" % identifier)
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	450 #end for
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	451 #else:
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	453 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
17 b484160969e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 16 diff changeset	454 ln -s "${f.bamfiles}" "./${counter}.bam" &&
b484160969e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 16 diff changeset	455 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	456 #silent $files.append('%s.bam' % $counter)
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	457 #silent $labels.append("'%s'" % $identifier)
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	458 #end for
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	459 #end if
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	460 ]]>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	461 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	462
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	463 <token name="@multiple_input_bigwigs@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	464 <![CDATA[
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	465 #set files=[]
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	466 #set labels=[]
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	467 #import re
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	468 #if $multibigwig_conditional.orderMatters == "No":
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	469 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	470 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	471 ln -s "${bigwig}" "${counter}.bw" &&
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	472 #silent $files.append('%s.bw' % $counter)
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	473 #silent $labels.append("'%s'" % $identifier)
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	474 #end for
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	475 #else:
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	476 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	477 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
17 b484160969e9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 16 diff changeset	478 ln -s "${f.bigwigfiles}" "${counter}.bw" &&
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	479 #silent $files.append('%s.bw' % $counter)
18 b72c892aefef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 17 diff changeset	480 #silent $labels.append("'%s'" % $identifier)
16 b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	481 #end for
b186037f17f1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 15 diff changeset	482 #end if
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	483 ]]>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	484 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	485
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	486 <xml name="blacklist">
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	487 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	488 label="Blacklisted regions in BED/GTF format"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	489 help="One or more files containing regions to exclude from the analysis" />
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	490 </xml>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	491
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	492 <token name="@blacklist@">
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	493 <![CDATA[
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	494 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	495 #set blfiles=[]
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	496 #for $f in $advancedOpt.blackListFileName:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	497 #silent $blfiles.append("'%s'" % $f)
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	498 #end for
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	499 #if $blfiles != ["'None'"]:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	500 --blackListFileName #echo ' '.join($blfiles)#
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	501 #end if
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	502 #end if
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	503 ]]>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	504 </token>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	505
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	506 <xml name="multiple_bed">
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	507 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	508 label="Regions in BED/GTF format"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	509 help="One or more files containing regions to include in the analysis" />
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	510 </xml>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	511
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	512 <token name="@multiple_bed@">
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	513 <![CDATA[
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	514 #set files=[]
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	515 #set labels=[]
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	516 #for $f in $BED:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	517 #silent $files.append("'%s'" % $f)
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	518 #silent $labels.append("'%s'" % $f.display_name)
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	519 #end for
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	520 #if len($files) > 0:
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	521 --BED #echo ' '.join($files)#
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	522 --regionLabels #echo ' '.join($labels)#
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	523 #end if
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	524 ]]>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	525 </token>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	526
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	527 <xml name="reference_genome_source">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	528 <conditional name="source">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	529 <param name="ref_source" type="select" label="Reference genome">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	530 <option value="cached">locally cached</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	531 <option value="history">in your history</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	532 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	533 <when value="cached">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	534 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	535 <options from_data_table="lastz_seqs">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	536 <filter type="sort_by" column="1" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	537 <validator type="no_options" message="No indexes are available." />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	538 </options>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	539 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	540 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	541 <when value="history">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	542 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	543 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	544 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	545 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	546
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	547 <token name="@reference_genome_source@">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	548 #if $source.ref_source=="history":
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	549 --genome $source.input1
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	550 #else:
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	551 --genome "$source.input1_2bit.fields.path"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	552 #end if
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	553 </token>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	554
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	555 <xml name="effectiveGenomeSize">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	556 <conditional name="effectiveGenomeSize">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	557 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	558 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.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	559 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	560 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.">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	561 <option value="93260000">ce10 (93260000)</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	562 <option value="121400000">dm3 (121400000)</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	563 <option value="2451960000" selected="true">hg19 (2451960000)</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	564 <option value="2150570000">mm9 (2150570000)</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	565 <option value="specific">user specified</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	566 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	567 <when value="specific">
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	568 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	569 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	570 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	571 <when value="2150570000" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	572 <when value="2451960000" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	573 <when value="121400000" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	574 <when value="93260000" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	575 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	576 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	577
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	578 <xml name="skipNAs">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	579 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	580 label="Ignore missing data?"
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	581 help="This parameter determines if non-covered regions
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	582 (regions without overlapping reads) in a bam/bigWig file
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	583 should be skipped. The default is to treat those
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	584 regions as having a value of zero. The decision to
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	585 skip non-covered regions depends on the interpretation
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	586 of the data. Non-covered regions may represent, for
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	587 example, repetitive regions that should be ignored.
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	588 (default: False)" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	589 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	590
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	591 <xml name="input_save_matrix_values">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	592 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	593 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	594
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	595 <xml name="input_graphic_output_settings">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	596 <conditional name="output" >
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	597 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	598 <option value="no" selected="true">no</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	599 <option value="yes">yes</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	600 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	601 <when value="no" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	602 <when value="yes">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	603 <yield />
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	604 <param name="saveSortedRegions" type="boolean"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	605 label="Save the regions after skipping zeros or min/max threshold values"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	606 help="The order of the regions in the file follows the sorting order selected. This is useful,
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	607 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	608 </when>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	609 </conditional>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	610 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	611
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	612
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	613 <xml name="input_image_file_format">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	614 <param argument="--outFileFormat" type="select" label="Image file format">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	615 <option value="png" selected="true">png</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	616 <option value="pdf">pdf</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	617 <option value="svg">svg</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	618 <option value="eps">eps</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	619 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	620 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	621
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	622 <xml name="output_dpi">
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	623 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	624 label="Image dpi" help=""/>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	625 </xml>
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	626
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	627 <xml name="output_image_file_format">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	628 <data format="png" name="outFileName" label="${tool.name} image">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	629 <change_format>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	630 <when input="output.outFileFormat" value="pdf" format="pdf" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	631 <when input="output.outFileFormat" value="svg" format="svg" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	632 <when input="output.outFileFormat" value="eps" format="eps" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	633 </change_format>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	634 </data>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	635 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	636
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	637 <xml name="output_image_file_format_not_nested">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	638 <data format="png" name="outFileName" label="${tool.name} image">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	639 <change_format>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	640 <when input="outFileFormat" value="pdf" format="pdf" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	641 <when input="outFileFormat" value="svg" format="svg" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	642 <when input="outFileFormat" value="eps" format="eps" />
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	643 </change_format>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	644 </data>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	645 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	646
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	647 <xml name="output_save_matrix_values">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	648 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	649 <filter>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	650 ((
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	651 output['showOutputSettings'] == 'yes' and
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	652 output['saveMatrix'] is True
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	653 ))
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	654 </filter>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	655 </data>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	656 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	657
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	658 <xml name="output_graphic_outputs">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	659 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	660 <filter>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	661 ((
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	662 output['showOutputSettings'] == 'yes' and
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	663 output['saveSortedRegions'] is True
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	664 ))
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	665 </filter>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	666 </data>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	667 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	668
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	669 <xml name="colorMap">
12 e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	670 <param name="colorMap" type="select" label="Color map to use for the heatmap"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	671 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
e9d7ac6f8e20 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296 bgruening parents: 11 diff changeset	672 multiple="true">
0 ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	673 <option value="RdYlBu" selected="true">RdYlBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	674 <option value="Accent">Accent</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	675 <option value="Spectral">Spectral</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	676 <option value="Set1">Set1</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	677 <option value="Set2">Set2</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	678 <option value="Set3">Set3</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	679 <option value="Dark2">Dark2</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	680 <option value="Reds">Reds</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	681 <option value="Oranges">Oranges</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	682 <option value="Greens">Greens</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	683 <option value="Blues">Blues</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	684 <option value="Greys">Greys</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	685 <option value="Purples">Purples</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	686 <option value="Paired">Paired</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	687 <option value="Pastel1">Pastel1</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	688 <option value="Pastel2">Pastel2</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	689 <option value="spring">spring</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	690 <option value="summer">summer</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	691 <option value="autumn">autumn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	692 <option value="winter">winter</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	693 <option value="hot">hot</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	694 <option value="coolwarm">coolwarm</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	695 <option value="cool">cool</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	696 <option value="seismic">seismic</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	697 <option value="terrain">terrain</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	698 <option value="ocean">ocean</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	699 <option value="rainbow">rainbow</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	700 <option value="bone">bone</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	701 <option value="flag">flag</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	702 <option value="prism">prism</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	703 <option value="cubehelix">cubehelix</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	704 <option value="binary">binary</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	705 <option value="pink">pink</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	706 <option value="gray">gray</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	707 <option value="copper">copper</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	708 <option value="BrBG">BrBG</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	709 <option value="BuGn">BuGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	710 <option value="BuPu">BuPu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	711 <option value="GnBu">GnBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	712 <option value="OrRd">OrRd</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	713 <option value="PiYG">PiYG</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	714 <option value="PRGn">PRGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	715 <option value="PuOr">PuOr</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	716 <option value="PuRd">PuRd</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	717 <option value="PuBu">PuBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	718 <option value="RdBu">RdBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	719 <option value="RdGy">RdGy</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	720 <option value="RdPu">RdPu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	721 <option value="YlGn">YlGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	722 <option value="PuBuGn">PuBuGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	723 <option value="RdYlGn">RdYlGn</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	724 <option value="YlGnBu">YlGnBu</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	725 <option value="YlOrBr">YlOrBr</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	726 <option value="YlOrRd">YlOrRd</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	727 <option value="gist_gray">gist_gray</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	728 <option value="gist_stern">gist_stern</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	729 <option value="gist_earth">gist_earth</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	730 <option value="gist_yarg">gist_yarg</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	731 <option value="gist_ncar">gist_ncar</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	732 <option value="gist_rainbow">gist_rainbow</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	733 <option value="gist_heat">gist_heat</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	734 <option value="gnuplot">gnuplot</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	735 <option value="gnuplot2">gnuplot2</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	736 <option value="CMRmap">CMRmap</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	737 <option value="bwr">bwr</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	738 <option value="hsv">hsv</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	739 <option value="brg">brg</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	740 <option value="jet">jet</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	741 <option value="afmhot">afmhot</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	742 <option value="Accent_r">Accent reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	743 <option value="Spectral_r">Spectral reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	744 <option value="Set1_r">Set1 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	745 <option value="Set2_r">Set2 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	746 <option value="Set3_r">Set3 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	747 <option value="Dark2_r">Dark2 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	748 <option value="Reds_r">Reds reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	749 <option value="Oranges_r">Oranges reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	750 <option value="Greens_r">Greens reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	751 <option value="Blues_r">Blues reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	752 <option value="Greys_r">Greys reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	753 <option value="Purples_r">Purples reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	754 <option value="Paired_r">Paired reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	755 <option value="Pastel1_r">Pastel1 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	756 <option value="Pastel2_r">Pastel2 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	757 <option value="spring_r">spring reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	758 <option value="summer_r">summer reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	759 <option value="autumn_r">autumn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	760 <option value="winter_r">winter reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	761 <option value="hot_r">hot reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	762 <option value="coolwarm_r">coolwarm reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	763 <option value="cool_r">cool reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	764 <option value="seismic_r">seismic reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	765 <option value="terrain_r">terrain reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	766 <option value="ocean_r">ocean reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	767 <option value="rainbow_r">rainbow reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	768 <option value="bone_r">bone reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	769 <option value="flag_r">flag reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	770 <option value="prism_r">prism reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	771 <option value="cubehelix_r">cubehelix reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	772 <option value="binary_r">binary reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	773 <option value="pink_r">pink reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	774 <option value="gray_r">gray reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	775 <option value="copper_r">copper reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	776 <option value="BrBG_r">BrBG reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	777 <option value="BuGn_r">BuGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	778 <option value="BuPu_r">BuPu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	779 <option value="GnBu_r">GnBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	780 <option value="OrRd_r">OrRd reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	781 <option value="PiYG_r">PiYG reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	782 <option value="PRGn_r">PRGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	783 <option value="PuOr_r">PuOr reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	784 <option value="PuRd_r">PuRd reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	785 <option value="PuBu_r">PuBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	786 <option value="RdBu_r">RdBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	787 <option value="RdGy_r">RdGy reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	788 <option value="RdPu_r">RdPu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	789 <option value="YlGn_r">YlGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	790 <option value="PuBuGn_r">PuBuGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	791 <option value="RdYlBu_r">RdYlBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	792 <option value="RdYlGn_r">RdYlGn reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	793 <option value="YlGnBu_r">YlGnBu reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	794 <option value="YlOrBr_r">YlOrBr reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	795 <option value="YlOrRd_r">YlOrRd reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	796 <option value="gist_gray_r">gist_gray reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	797 <option value="gist_stern_r">gist_stern reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	798 <option value="gist_earth_r">gist_earth reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	799 <option value="gist_yarg_r">gist_yarg reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	800 <option value="gist_ncar_r">gist_ncar reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	801 <option value="gist_rainbow_r">gist_rainbow reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	802 <option value="gist_heat_r">gist_heat reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	803 <option value="gnuplot_r">gnuplot reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	804 <option value="gnuplot2_r">gnuplot2 reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	805 <option value="CMRmap_r">CMRmap reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	806 <option value="bwr_r">bwr reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	807 <option value="hsv_r">hsv reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	808 <option value="brg_r">brg reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	809 <option value="jet_r">jet reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	810 <option value="afmhot_r">afmhot reversed</option>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	811 </param>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	812
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	813 </xml>
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	814
ca581d3634d1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20' bgruening parents: diff changeset	815 </macros>

Mercurial > repos > bgruening > deeptools_multi_bigwig_summary

annotate deepTools_macros.xml @ 18:b72c892aefef draft