annotate deepTools_macros.xml @ 2:8e57345c05ef draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 08:10:09 -0500
parents a1124c201eee
children c1bc2d0c2e5b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
1 <macros>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
2
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
3 <xml name="advancedOpt_scaffold">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
4 <conditional name="advancedOpt">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
6 <option value="no" selected="true">no</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
7 <option value="yes">yes</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
8 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
9 <when value="no" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
10 <when value="yes">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
11 <yield/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
12 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
13 </conditional>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
14 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
15
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
20 --extendReads
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
21 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
22 $advancedOpt.ignoreDuplicates
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
23 $advancedOpt.centerReads
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
24 #if $advancedOpt.minMappingQuality:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
25 --minMappingQuality '$advancedOpt.minMappingQuality'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
26 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
27 #if $advancedOpt.samFlagInclude:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
28 --samFlagInclude $advancedOpt.samFlagInclude
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
29 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
30 #if $advancedOpt.samFlagExclude:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
31 --samFlagExclude $advancedOpt.samFlagExclude
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
32 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
33 #if $advancedOpt.minFragmentLength:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
34 --minFragmentLength $advancedOpt.minFragmentLength
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
35 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
36 #if $advancedOpt.maxFragmentLength:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
37 --maxFragmentLength $advancedOpt.maxFragmentLength
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
38 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
39 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
40
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
41 <token name="@ADVANCED_OPTS_GTF@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
42 $advancedOpt.metagene
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
43 #if $advancedOpt.transcriptID:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
44 --transcriptID $advancedOpt.transcriptID
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
45 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
46 #if $advancedOpt.exonID:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
47 --exonID $advancedOpt.exonID
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
48 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
49 #if $advancedOpt.transcript_id_designator:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
50 --transcript_id_designator $advancedOpt.transcript_id_designator
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
51 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
52 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
53
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
54 <xml name="heatmap_options">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
55 <expand macro="zMin_zMax" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
56 <expand macro="colorMap" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
57 <expand macro="plotTitle" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
58 <expand macro="plotNumbers" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
59 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
60
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
61 <token name="@HEATMAP_OPTIONS@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
62 #if str($plotting_type.zMin) != "":
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
63 --zMin $plotting_type.zMin
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
64 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
65 #if str($plotting_type.zMax) != "":
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
66 --zMax $plotting_type.zMax
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
67 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
68 --colorMap '$plotting_type.colorMap'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
69 $plotting_type.plotNumbers
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
70 --plotTitle '$plotting_type.plotTitle'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
71 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
72
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
73
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
74 <xml name="includeZeros">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
75 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
76 label="Include zeros"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
77 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
78 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
79
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
80 <xml name="zMin_zMax">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
81 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
82 help="If not specified the value is set automatically."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
83 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
84 help="If not specified the value is set automatically."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
85 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
86
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
87 <xml name="region_limit_operation">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
88 <param argument="--region" type="text" value=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
89 label="Region of the genome to limit the operation to"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
90 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
91 <sanitizer>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
92 <valid initial="string.letters,string.digits">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
93 <add value="|"/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
94 <add value=":"/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
95 </valid>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
96 </sanitizer>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
97 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
98 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
99
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
100 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
101 <token name="@WRAPPER_VERSION@">2.4.1</token>
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
102 <xml name="requirements">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
103 <requirements>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
104 <requirement type="package" version="2.7.10">python</requirement>
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
105 <requirement type="package" version="2.4.1">deeptools</requirement>
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
106 <yield />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
107 </requirements>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
108 <expand macro="stdio" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
109 <version_command>@BINARY@ --version</version_command>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
110 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
111
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
112 <xml name="smoothLength">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
114 label="Smooth values using the following length (in bases)"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
116 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
117
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
118
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
119 <xml name="kmeans_clustering">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
120 <conditional name="used_multiple_regions">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
121 <param name="used_multiple_regions_options" type="select"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
122 label="Did you compute the matrix with more than one groups of regions?"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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.">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
124 <option value="yes">Yes, I used multiple groups of regions</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
125 <option value="no">No, I used only one group</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
126 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
127 <when value="no">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
128 <conditional name="clustering">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
129 <param name="clustering_options" type="select" label="Clustering algorithm">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
130 <option value="none">No clustering</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
131 <option value="kmeans">Kmeans clustering</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
132 <option value="hclust">Hierarchical clustering</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
133 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
134 <when value="kmeans">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
135 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
136 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
137 This only works for data that is not grouped, otherwise only the first group will be clustered.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
138 If more specific clustering methods are required it is advisable to save the underlying matrix and
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
139 run the clustering using other software."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
140 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
141 <when value="hclust">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
142 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
143 help="WARNING: This option causes the tool to run for a very long time! When this option is
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
144 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
145 This only works for data that is not grouped, otherwise only the first group will be clustered.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
146 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
147 If more specific clustering methods are required it is advisable to save the underlying matrix and
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
148 run the clustering using other software."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
149 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
150 <when value="none" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
151 </conditional>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
152 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
153 <when value="yes" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
154 </conditional>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
155 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
156
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
157 <token name="@KMEANS_CLUSTERING@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
158 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
159 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
160 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
161 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
162 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
163 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
164 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
165 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
166 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
167 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
168 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
169 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
170 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
171
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
172 <xml name="samFlags">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
173 <param argument="--samFlagInclude" type="integer" optional="True" value=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
174 label="Include reads based on the SAM flag"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
176 <param argument="--samFlagExclude" type="integer" optional="True" value=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
177 label="Exclude reads based on the SAM flag"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
179 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
180
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
181 <xml name="fragLength">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
183 label="Minimum fragment length for inclusion."
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
184 help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
186 label="Maximum fragment length for inclusion."
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
187 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
188 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
189
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
190 <xml name="read_processing_options">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
191 <expand macro="extendReads" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
192 <expand macro="ignoreDuplicates" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
193 <expand macro="centerReads" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
194 <expand macro="minMappingQuality" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
195 <expand macro="samFlags" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
196 <expand macro="fragLength" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
197 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
198
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
199 <xml name="gtf_options">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
200 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
201 label="Use a metagene model"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
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." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
203 <param argument="--transcriptID" optional="True" value="transcript" type="text"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
204 label="trascript designator"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
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" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
206 <param argument="--exonID" optional="True" value="exon" type="text"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
207 label="exon designator"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
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" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
209 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
210 label="transcriptID key designator"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
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)
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
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.,
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
213 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
214 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
215 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
216
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
217
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
218 <xml name="plotNumbers">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
219 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
220 label="Plot the correlation value"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
221 help="If set, then the correlation number is plotted on top of the heatmap."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
222 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
223
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
224 <xml name="extendReads">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
225 <conditional name="doExtendCustom">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
226 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
228 By default *each* read mate is extended.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
230 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
232 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
233 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
234 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
235 <option value="custom">A custom length, which will be applied to ALL reads.</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
236 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
237 <when value="no" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
238 <when value="yes" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
239 <when value="custom">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
240 <param name="extendReadsValue" type="integer" value="300" min="1"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
241 label="Extend reads to the given average fragment size"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
242 help="Extend all reads to this length" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
243 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
244 </conditional>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
245 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
246
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
247 <xml name="corMethod">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
248 <param argument="--corMethod" type="select" label="Correlation method">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
249 <option value="spearman" selected="True">Spearman</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
250 <option value="pearson">Pearson</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
251 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
252 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
253
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
254 <xml name="distanceBetweenBins">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
255 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
256 label="Distance between bins"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
257 help="By default, multiBamSummary considers consecutive bins of
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
258 the specified 'Bin size'. However, to reduce the
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
259 computation time, a larger distance between bins can
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
260 be given. Larger distances result in fewer bins being
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
261 considered."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
262 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
263
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
264 <xml name="centerReads">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
265 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
266 label="Center regions with respect to the fragment length"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
268 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
269
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
270 <xml name="ignoreDuplicates">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
271 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
272 label="Ignore duplicates"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
274 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
275
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
276 <xml name="sortUsing">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
277 <param argument="--sortUsing" type="select" label="Method used for sorting"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
278 help="For each row the method is computed.">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
279 <option value="mean" selected="true">mean</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
280 <option value="median">median</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
281 <option value="min">min</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
282 <option value="max">max</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
283 <option value="sum">sum</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
284 <option value="region_length">region length</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
285 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
286 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
287
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
288 <xml name="sortRegionsComputeMatrix">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
289 <param argument="--sortRegions" type="select" label="Sort regions"
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
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.">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
291 <option value="no">no ordering</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
292 <option value="keep" selected="true">maintain the same ordering as the input files</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
293 <option value="descend">descending order</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
294 <option value="ascend">ascending order</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
295 </param>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
296 </xml>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
297
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
298 <xml name="sortRegions">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
299 <param argument="--sortRegions" type="select" label="Sort regions"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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.">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
301 <option value="no">no ordering</option>
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
302 <option value="descend">descending order</option>
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
303 <option value="ascend">ascending order</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
304 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
305 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
306
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
307 <xml name="minMappingQuality">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
308 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
309 label="Minimum mapping quality"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
310 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
311 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
312
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
313 <xml name="skipZeros">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
314 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
315 label ="Skip zeros"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
317 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
318
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
319 <xml name="fragmentLength">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
320 <param argument="--fragmentLength" type="integer" value="300" min="1"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
321 label="Fragment length used for the sequencing"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
323 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
324
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
325 <xml name="scaleFactor">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
326 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
327 help="When used in combination with --normalizeTo1x or
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
328 --normalizeUsingRPKM, the computed scaling factor will
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
329 be multiplied by the given scale factor." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
330 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
331
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
332 <xml name="scaleFactors">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
333 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
334 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
335 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
336
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
337 <xml name="stdio">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
338 <stdio>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
339 <exit_code range="1:" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
340 <exit_code range=":-1" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
341 <regex match="Error:" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
342 <regex match="Exception:" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
343 <regex match="EXception:" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
344 <regex match="Traceback" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
345 </stdio>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
346 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
347
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
348 <xml name="pseudocount">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
349 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
350 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
351
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
352 <token name="@REFERENCES@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
353
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
354 .. class:: infomark
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
355
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
356 For more information on the tools, please visit our `help site`_.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
357
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
358 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
359
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
360 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
361
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
362 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
363 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
364 .. _help site: https://deeptools.readthedocs.org/
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
365
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
366 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
367 <xml name="citations">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
368 <citations>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
369 <citation type="doi">10.1093/nar/gkw257</citation>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
370 <yield />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
371 </citations>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
372 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
373
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
374 <xml name="multiple_input_bams">
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
375 <conditional name="multibam_conditional">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
376 <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.">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
377 <option value="No" selected="true">No</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
378 <option value="Yes">Yes</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
379 </param>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
380 <when value="No">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
381 <param argument="--bamfiles" type="data" format="bam" min="1"
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
382 label="Bam file" multiple="true"
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
383 help=""/>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
384 </when>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
385 <when value="Yes">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
386 <repeat name="multibam_repeats" min="1" title="BAM Files">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
387 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
388 </repeat>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
389 </when>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
390 </conditional>
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
391 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
392
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
393 <xml name="multiple_input_bams_min2">
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
394 <conditional name="multibam_conditional">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
395 <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
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
396 is vital to you, select Yes below.">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
397 <option value="No" selected="true">No</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
398 <option value="Yes">Yes</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
399 </param>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
400 <when value="No">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
401 <param argument="--bamfiles" type="data" format="bam" min="2"
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
402 label="Bam file" multiple="true"
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
403 help=""/>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
404 </when>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
405 <when value="Yes">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
406 <repeat name="multibam_repeats" min="2" title="BAM Files">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
407 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
408 </repeat>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
409 </when>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
410 </conditional>
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
411 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
412
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
413 <xml name="multiple_input_bigwigs">
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
414 <conditional name="multibigwig_conditional">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
415 <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
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
416 is vital to you, select Yes below.">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
417 <option value="No" selected="true">No</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
418 <option value="Yes">Yes</option>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
419 </param>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
420 <when value="No">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
421 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
422 label="Bigwig file"
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
423 help="A Bigwig file."/>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
424 </when>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
425 <when value="Yes">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
426 <repeat name="multibigwig_repeats" min="2" title="BigWig files">
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
427 <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
428 </repeat>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
429 </when>
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
430 </conditional>
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
431 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
432
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
433 <xml name="plotTitle">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
434 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
435 label="Title of the plot"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
436 help="Title of the plot, to be printed on top of the generated image." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
437 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
438
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
439
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
440 <token name="@multiple_input_bams@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
441 <![CDATA[
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
442 #set files=[]
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
443 #set labels=[]
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
444 #if $multibam_conditional.orderMatters == "No":
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
445 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
446 ln -s "${bamfile}" "./${counter}.bam" &&
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
448 #silent $files.append('%s.bam' % $counter)
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
449 #silent $labels.append("'%s'" % ($bamfile.display_name))
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
450 #end for
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
451 #else:
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
453 ln -s "${f.bamfile}" "./${counter}.bam" &&
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
454 ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
455 #silent $files.append('%s.bam' % $counter)
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
456 #silent $labels.append("'%s'" % ($f.bamfile.display_name))
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
457 #end for
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
458 #end if
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
459 ]]>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
460 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
461
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
462 <token name="@multiple_input_bigwigs@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
463 <![CDATA[
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
464 #set files=[]
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
465 #set labels=[]
2
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
466 #if $multibigwig_conditional.orderMatters == "No":
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
467 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
468 ln -s "${bigwig}" "${counter}.bw" &&
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
469 #silent $files.append('%s.bw' % $counter)
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
470 #silent $labels.append("'%s'" % ($bigwig.display_name))
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
471 #end for
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
472 #else:
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
473 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
474 ln -s "${f.bigwig}" "${counter}.bw" &&
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
475 #silent $files.append('%s.bw' % $counter)
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
476 #silent $labels.append("'%s'" % ($f.bigwig.display_name))
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
477 #end for
8e57345c05ef planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 1
diff changeset
478 #end if
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
479 ]]>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
480 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
481
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
482 <xml name="blacklist">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
483 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
484 label="Blacklisted regions in BED/GTF format"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
485 help="One or more files containing regions to exclude from the analysis" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
486 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
487
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
488 <token name="@blacklist@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
489 <![CDATA[
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
490 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
491 #set blfiles=[]
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
492 #for $f in $advancedOpt.blackListFileName:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
493 #silent $blfiles.append("'%s'" % $f)
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
494 #end for
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
495 #if $blfiles != ["'None'"]:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
496 --blackListFileName #echo ' '.join($blfiles)#
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
497 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
498 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
499 ]]>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
500 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
501
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
502 <xml name="multiple_bed">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
503 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
504 label="Regions in BED/GTF format"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
505 help="One or more files containing regions to include in the analysis" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
506 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
507
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
508 <token name="@multiple_bed@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
509 <![CDATA[
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
510 #set files=[]
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
511 #set labels=[]
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
512 #for $f in $BED:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
513 #silent $files.append("'%s'" % $f)
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
514 #silent $labels.append("'%s'" % $f.display_name)
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
515 #end for
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
516 #if len($files) > 0:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
517 --BED #echo ' '.join($files)#
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
518 --regionLabels #echo ' '.join($labels)#
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
519 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
520 ]]>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
521 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
522
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
523 <xml name="reference_genome_source">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
524 <conditional name="source">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
525 <param name="ref_source" type="select" label="Reference genome">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
526 <option value="cached">locally cached</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
527 <option value="history">in your history</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
528 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
529 <when value="cached">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
530 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
531 <options from_data_table="lastz_seqs">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
532 <filter type="sort_by" column="1" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
533 <validator type="no_options" message="No indexes are available." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
534 </options>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
535 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
536 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
537 <when value="history">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
538 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
539 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
540 </conditional>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
541 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
542
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
543 <token name="@reference_genome_source@">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
544 #if $source.ref_source=="history":
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
545 --genome $source.input1
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
546 #else:
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
547 --genome "$source.input1_2bit.fields.path"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
548 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
549 </token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
550
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
551 <xml name="effectiveGenomeSize">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
552 <conditional name="effectiveGenomeSize">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
553 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
554 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.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
555 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
556 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.">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
557 <option value="93260000">ce10 (93260000)</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
558 <option value="121400000">dm3 (121400000)</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
559 <option value="2451960000" selected="true">hg19 (2451960000)</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
560 <option value="2150570000">mm9 (2150570000)</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
561 <option value="specific">user specified</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
562 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
563 <when value="specific">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
564 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
565 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
566 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
567 <when value="2150570000" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
568 <when value="2451960000" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
569 <when value="121400000" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
570 <when value="93260000" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
571 </conditional>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
572 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
573
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
574 <xml name="skipNAs">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
575 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
576 label="Ignore missing data?"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
577 help="This parameter determines if non-covered regions
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
578 (regions without overlapping reads) in a bam/bigWig file
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
579 should be skipped. The default is to treat those
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
580 regions as having a value of zero. The decision to
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
581 skip non-covered regions depends on the interpretation
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
582 of the data. Non-covered regions may represent, for
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
583 example, repetitive regions that should be ignored.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
584 (default: False)" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
585 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
586
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
587 <xml name="input_save_matrix_values">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
588 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
589 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
590
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
591 <xml name="input_graphic_output_settings">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
592 <conditional name="output" >
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
593 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
594 <option value="no" selected="true">no</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
595 <option value="yes">yes</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
596 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
597 <when value="no" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
598 <when value="yes">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
599 <yield />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
600 <param name="saveSortedRegions" type="boolean"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
601 label="Save the regions after skipping zeros or min/max threshold values"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
602 help="The order of the regions in the file follows the sorting order selected. This is useful,
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
603 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
604 </when>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
605 </conditional>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
606 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
607
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
608
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
609 <xml name="input_image_file_format">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
610 <param argument="--outFileFormat" type="select" label="Image file format">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
611 <option value="png" selected="true">png</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
612 <option value="pdf">pdf</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
613 <option value="svg">svg</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
614 <option value="eps">eps</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
615 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
616 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
617
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
618 <xml name="output_dpi">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
619 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
620 label="Image dpi" help=""/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
621 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
622
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
623 <xml name="output_image_file_format">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
624 <data format="png" name="outFileName" label="${tool.name} image">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
625 <change_format>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
626 <when input="output.outFileFormat" value="pdf" format="pdf" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
627 <when input="output.outFileFormat" value="svg" format="svg" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
628 <when input="output.outFileFormat" value="eps" format="eps" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
629 </change_format>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
630 </data>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
631 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
632
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
633 <xml name="output_image_file_format_not_nested">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
634 <data format="png" name="outFileName" label="${tool.name} image">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
635 <change_format>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
636 <when input="outFileFormat" value="pdf" format="pdf" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
637 <when input="outFileFormat" value="svg" format="svg" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
638 <when input="outFileFormat" value="eps" format="eps" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
639 </change_format>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
640 </data>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
641 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
642
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
643 <xml name="output_save_matrix_values">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
644 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
645 <filter>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
646 ((
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
647 output['showOutputSettings'] == 'yes' and
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
648 output['saveMatrix'] is True
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
649 ))
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
650 </filter>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
651 </data>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
652 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
653
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
654 <xml name="output_graphic_outputs">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
655 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
656 <filter>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
657 ((
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
658 output['showOutputSettings'] == 'yes' and
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
659 output['saveSortedRegions'] is True
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
660 ))
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
661 </filter>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
662 </data>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
663 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
664
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
665 <xml name="colorMap">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
666 <param name="colorMap" type="select" label="Color map to use for the heatmap"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
667 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
668 multiple="true">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
669 <option value="RdYlBu" selected="true">RdYlBu</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
670 <option value="Accent">Accent</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
671 <option value="Spectral">Spectral</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
672 <option value="Set1">Set1</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
673 <option value="Set2">Set2</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
674 <option value="Set3">Set3</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
675 <option value="Dark2">Dark2</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
676 <option value="Reds">Reds</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
677 <option value="Oranges">Oranges</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
678 <option value="Greens">Greens</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
679 <option value="Blues">Blues</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
680 <option value="Greys">Greys</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
681 <option value="Purples">Purples</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
682 <option value="Paired">Paired</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
683 <option value="Pastel1">Pastel1</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
684 <option value="Pastel2">Pastel2</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
685 <option value="spring">spring</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
686 <option value="summer">summer</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
687 <option value="autumn">autumn</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
688 <option value="winter">winter</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
689 <option value="hot">hot</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
690 <option value="coolwarm">coolwarm</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
691 <option value="cool">cool</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
692 <option value="seismic">seismic</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
693 <option value="terrain">terrain</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
694 <option value="ocean">ocean</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
695 <option value="rainbow">rainbow</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
696 <option value="bone">bone</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
697 <option value="flag">flag</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
698 <option value="prism">prism</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
699 <option value="cubehelix">cubehelix</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
700 <option value="binary">binary</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
701 <option value="pink">pink</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
702 <option value="gray">gray</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
703 <option value="copper">copper</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
704 <option value="BrBG">BrBG</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
705 <option value="BuGn">BuGn</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
706 <option value="BuPu">BuPu</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
707 <option value="GnBu">GnBu</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
708 <option value="OrRd">OrRd</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
709 <option value="PiYG">PiYG</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
710 <option value="PRGn">PRGn</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
711 <option value="PuOr">PuOr</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
712 <option value="PuRd">PuRd</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
713 <option value="PuBu">PuBu</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
714 <option value="RdBu">RdBu</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
715 <option value="RdGy">RdGy</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
716 <option value="RdPu">RdPu</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
717 <option value="YlGn">YlGn</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
718 <option value="PuBuGn">PuBuGn</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
719 <option value="RdYlGn">RdYlGn</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
720 <option value="YlGnBu">YlGnBu</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
721 <option value="YlOrBr">YlOrBr</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
722 <option value="YlOrRd">YlOrRd</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
723 <option value="gist_gray">gist_gray</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
724 <option value="gist_stern">gist_stern</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
725 <option value="gist_earth">gist_earth</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
726 <option value="gist_yarg">gist_yarg</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
727 <option value="gist_ncar">gist_ncar</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
728 <option value="gist_rainbow">gist_rainbow</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
729 <option value="gist_heat">gist_heat</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
730 <option value="gnuplot">gnuplot</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
731 <option value="gnuplot2">gnuplot2</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
732 <option value="CMRmap">CMRmap</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
733 <option value="bwr">bwr</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
734 <option value="hsv">hsv</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
735 <option value="brg">brg</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
736 <option value="jet">jet</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
737 <option value="afmhot">afmhot</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
738 <option value="Accent_r">Accent reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
739 <option value="Spectral_r">Spectral reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
740 <option value="Set1_r">Set1 reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
741 <option value="Set2_r">Set2 reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
742 <option value="Set3_r">Set3 reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
743 <option value="Dark2_r">Dark2 reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
744 <option value="Reds_r">Reds reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
745 <option value="Oranges_r">Oranges reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
746 <option value="Greens_r">Greens reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
747 <option value="Blues_r">Blues reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
748 <option value="Greys_r">Greys reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
749 <option value="Purples_r">Purples reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
750 <option value="Paired_r">Paired reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
751 <option value="Pastel1_r">Pastel1 reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
752 <option value="Pastel2_r">Pastel2 reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
753 <option value="spring_r">spring reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
754 <option value="summer_r">summer reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
755 <option value="autumn_r">autumn reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
756 <option value="winter_r">winter reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
757 <option value="hot_r">hot reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
758 <option value="coolwarm_r">coolwarm reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
759 <option value="cool_r">cool reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
760 <option value="seismic_r">seismic reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
761 <option value="terrain_r">terrain reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
762 <option value="ocean_r">ocean reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
763 <option value="rainbow_r">rainbow reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
764 <option value="bone_r">bone reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
765 <option value="flag_r">flag reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
766 <option value="prism_r">prism reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
767 <option value="cubehelix_r">cubehelix reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
768 <option value="binary_r">binary reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
769 <option value="pink_r">pink reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
770 <option value="gray_r">gray reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
771 <option value="copper_r">copper reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
772 <option value="BrBG_r">BrBG reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
773 <option value="BuGn_r">BuGn reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
774 <option value="BuPu_r">BuPu reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
775 <option value="GnBu_r">GnBu reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
776 <option value="OrRd_r">OrRd reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
777 <option value="PiYG_r">PiYG reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
778 <option value="PRGn_r">PRGn reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
779 <option value="PuOr_r">PuOr reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
780 <option value="PuRd_r">PuRd reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
781 <option value="PuBu_r">PuBu reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
782 <option value="RdBu_r">RdBu reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
783 <option value="RdGy_r">RdGy reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
784 <option value="RdPu_r">RdPu reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
785 <option value="YlGn_r">YlGn reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
786 <option value="PuBuGn_r">PuBuGn reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
787 <option value="RdYlBu_r">RdYlBu reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
788 <option value="RdYlGn_r">RdYlGn reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
789 <option value="YlGnBu_r">YlGnBu reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
790 <option value="YlOrBr_r">YlOrBr reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
791 <option value="YlOrRd_r">YlOrRd reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
792 <option value="gist_gray_r">gist_gray reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
793 <option value="gist_stern_r">gist_stern reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
794 <option value="gist_earth_r">gist_earth reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
795 <option value="gist_yarg_r">gist_yarg reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
796 <option value="gist_ncar_r">gist_ncar reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
797 <option value="gist_rainbow_r">gist_rainbow reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
798 <option value="gist_heat_r">gist_heat reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
799 <option value="gnuplot_r">gnuplot reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
800 <option value="gnuplot2_r">gnuplot2 reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
801 <option value="CMRmap_r">CMRmap reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
802 <option value="bwr_r">bwr reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
803 <option value="hsv_r">hsv reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
804 <option value="brg_r">brg reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
805 <option value="jet_r">jet reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
806 <option value="afmhot_r">afmhot reversed</option>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
807 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
808
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
809 </xml>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
810
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
811 </macros>