annotate deepTools_macros.xml @ 13:b8431744eab3 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
author bgruening
date Fri, 31 Mar 2017 18:13:32 -0400
parents 94b05ea80203
children d4fdd10516f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
1 <macros>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
2
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
4 <token name="@WRAPPER_VERSION@">2.5.0</token>
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
5 <xml name="requirements">
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
6 <requirements>
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
7 <requirement type="package" version="2.7.10">python</requirement>
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
8 <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
9 <yield />
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
10 </requirements>
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
11 <expand macro="stdio" />
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
12 <version_command>@BINARY@ --version</version_command>
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
13 </xml>
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
14
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
15 <xml name="advancedOpt_scaffold">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
16 <conditional name="advancedOpt">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
17 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
18 <option value="no" selected="true">no</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
19 <option value="yes">yes</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
20 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
21 <when value="no" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
22 <when value="yes">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
23 <yield/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
24 </when>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
25 </conditional>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
26 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
27
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
28 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
29 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
30 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
31 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
32 --extendReads
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
33 #end if
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
34 $advancedOpt.ignoreDuplicates
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
35 $advancedOpt.centerReads
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
36 #if $advancedOpt.minMappingQuality:
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
37 --minMappingQuality '$advancedOpt.minMappingQuality'
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
38 #end if
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
39 #if $advancedOpt.samFlagInclude:
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
40 --samFlagInclude $advancedOpt.samFlagInclude
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
41 #end if
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
42 #if $advancedOpt.samFlagExclude:
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
43 --samFlagExclude $advancedOpt.samFlagExclude
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
44 #end if
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
45 #if $advancedOpt.minFragmentLength:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
46 --minFragmentLength $advancedOpt.minFragmentLength
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
47 #end if
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
48 #if $advancedOpt.maxFragmentLength:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
49 --maxFragmentLength $advancedOpt.maxFragmentLength
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
50 #end if
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
51 </token>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
52
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
53 <token name="@ADVANCED_OPTS_GTF@">
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
54 $advancedOpt.metagene
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
55 #if $advancedOpt.transcriptID:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
56 --transcriptID $advancedOpt.transcriptID
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
57 #end if
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
58 #if $advancedOpt.exonID:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
59 --exonID $advancedOpt.exonID
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
60 #end if
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
61 #if $advancedOpt.transcript_id_designator:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
62 --transcript_id_designator $advancedOpt.transcript_id_designator
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
63 #end if
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
64 </token>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
65
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
66 <xml name="heatmap_options">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
67 <expand macro="zMin_zMax" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
68 <expand macro="colorMap" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
69 <expand macro="plotTitle" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
70 <expand macro="plotNumbers" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
71 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
72
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
73 <token name="@HEATMAP_OPTIONS@">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
74 #if str($plotting_type.zMin) != "":
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
75 --zMin $plotting_type.zMin
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
76 #end if
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
77 #if str($plotting_type.zMax) != "":
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
78 --zMax $plotting_type.zMax
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
79 #end if
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
80 --colorMap '$plotting_type.colorMap'
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
81 $plotting_type.plotNumbers
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
82 --plotTitle '$plotting_type.plotTitle'
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
83 </token>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
84
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
85
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
86 <xml name="includeZeros">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
87 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
88 label="Include zeros"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
89 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
90 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
91
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
92 <xml name="zMin_zMax">
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
93 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
94 help="If not specified the value is set automatically."/>
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
95 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
96 help="If not specified the value is set automatically."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
97 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
98
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
99 <xml name="region_limit_operation">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
100 <param argument="--region" type="text" value=""
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
101 label="Region of the genome to limit the operation to"
6
6a077ef72dd4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 5
diff changeset
102 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;.">
6a077ef72dd4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 5
diff changeset
103 <sanitizer>
6a077ef72dd4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 5
diff changeset
104 <valid initial="string.letters,string.digits">
6a077ef72dd4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 5
diff changeset
105 <add value="|"/>
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
106 <add value=":"/>
6
6a077ef72dd4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 5
diff changeset
107 </valid>
6a077ef72dd4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 5
diff changeset
108 </sanitizer>
6a077ef72dd4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 5
diff changeset
109 </param>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
110 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
111
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
112 <xml name="smoothLength">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
114 label="Smooth values using the following length (in bases)"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
116 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
117
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
118
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
119 <xml name="kmeans_clustering">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
120 <conditional name="used_multiple_regions">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
121 <param name="used_multiple_regions_options" type="select"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
122 label="Did you compute the matrix with more than one groups of regions?"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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.">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
124 <option value="yes">Yes, I used multiple groups of regions</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
125 <option value="no">No, I used only one group</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
126 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
127 <when value="no">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
128 <conditional name="clustering">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
129 <param name="clustering_options" type="select" label="Clustering algorithm">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
130 <option value="none">No clustering</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
131 <option value="kmeans">Kmeans clustering</option>
1
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
132 <option value="hclust">Hierarchical clustering</option>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
133 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
134 <when value="kmeans">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
135 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
136 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
137 This only works for data that is not grouped, otherwise only the first group will be clustered.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
138 If more specific clustering methods are required it is advisable to save the underlying matrix and
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
139 run the clustering using other software."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
140 </when>
1
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
141 <when value="hclust">
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
142 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
143 help="WARNING: This option causes the tool to run for a very long time! When this option is
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
144 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
145 This only works for data that is not grouped, otherwise only the first group will be clustered.
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
146 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
147 If more specific clustering methods are required it is advisable to save the underlying matrix and
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
148 run the clustering using other software."/>
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
149 </when>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
150 <when value="none" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
151 </conditional>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
152 </when>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
153 <when value="yes" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
154 </conditional>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
155 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
156
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
157 <token name="@KMEANS_CLUSTERING@">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
158 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
159 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
160 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
161 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
162 #end if
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
163 #end if
1
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
164 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
165 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
166 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
167 #end if
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
168 #end if
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
169 #end if
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
170 </token>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
171
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
172 <xml name="samFlags">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
173 <param argument="--samFlagInclude" type="integer" optional="True" value=""
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
174 label="Include reads based on the SAM flag"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
176 <param argument="--samFlagExclude" type="integer" optional="True" value=""
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
177 label="Exclude reads based on the SAM flag"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
179 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
180
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
181 <xml name="fragLength">
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
183 label="Minimum fragment length for inclusion."
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
184 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
186 label="Maximum fragment length for inclusion."
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
187 help="A value of 0 (the default) is equivalent to no maximum." />
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
188 </xml>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
189
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
190 <xml name="read_processing_options">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
191 <expand macro="extendReads" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
192 <expand macro="ignoreDuplicates" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
193 <expand macro="centerReads" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
194 <expand macro="minMappingQuality" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
195 <expand macro="samFlags" />
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
196 <expand macro="fragLength" />
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
197 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
198
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
199 <xml name="gtf_options">
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
200 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
201 label="Use a metagene model"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
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." />
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
203 <param argument="--transcriptID" optional="True" value="transcript" type="text"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
204 label="trascript designator"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
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" />
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
206 <param argument="--exonID" optional="True" value="exon" type="text"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
207 label="exon designator"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
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" />
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
209 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
210 label="transcriptID key designator"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
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)
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
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.,
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
213 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
214 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
215 </xml>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
216
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
217
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
218 <xml name="plotNumbers">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
219 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
220 label="Plot the correlation value"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
221 help="If set, then the correlation number is plotted on top of the heatmap."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
222 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
223
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
224 <xml name="extendReads">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
225 <conditional name="doExtendCustom">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
226 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
228 By default *each* read mate is extended.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
230 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
232 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
233 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
234 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
235 <option value="custom">A custom length, which will be applied to ALL reads.</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
236 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
237 <when value="no" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
238 <when value="yes" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
239 <when value="custom">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
240 <param name="extendReadsValue" type="integer" value="300" min="1"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
241 label="Extend reads to the given average fragment size"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
242 help="Extend all reads to this length" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
243 </when>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
244 </conditional>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
245 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
246
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
247 <xml name="corMethod">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
248 <param argument="--corMethod" type="select" label="Correlation method">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
249 <option value="spearman" selected="True">Spearman</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
250 <option value="pearson">Pearson</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
251 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
252 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
253
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
254 <xml name="distanceBetweenBins">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
255 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
256 label="Distance between bins"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
257 help="By default, multiBamSummary considers consecutive bins of
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
258 the specified 'Bin size'. However, to reduce the
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
259 computation time, a larger distance between bins can
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
260 be given. Larger distances result in fewer bins being
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
261 considered."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
262 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
263
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
264 <xml name="centerReads">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
265 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
266 label="Center regions with respect to the fragment length"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
268 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
269
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
270 <xml name="ignoreDuplicates">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
271 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
272 label="Ignore duplicates"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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." />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
274 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
275
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
276 <xml name="sortUsing">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
277 <param argument="--sortUsing" type="select" label="Method used for sorting"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
278 help="For each row the method is computed.">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
279 <option value="mean" selected="true">mean</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
280 <option value="median">median</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
281 <option value="min">min</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
282 <option value="max">max</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
283 <option value="sum">sum</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
284 <option value="region_length">region length</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
285 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
286 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
287
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
288 <xml name="sortRegionsComputeMatrix">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
289 <param argument="--sortRegions" type="select" label="Sort regions"
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
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.">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
291 <option value="no">no ordering</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
292 <option value="keep" selected="true">maintain the same ordering as the input files</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
293 <option value="descend">descending order</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
294 <option value="ascend">ascending order</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
295 </param>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
296 </xml>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
297
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
298 <xml name="sortRegions">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
299 <param argument="--sortRegions" type="select" label="Sort regions"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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.">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
301 <option value="no">no ordering</option>
11
4ae546bddd00 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
bgruening
parents: 10
diff changeset
302 <option value="descend" selected="true">descending order</option>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
303 <option value="ascend">ascending order</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
304 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
305 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
306
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
307 <xml name="minMappingQuality">
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
308 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
309 label="Minimum mapping quality"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
310 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
311 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
312
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
313 <xml name="skipZeros">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
314 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
315 label ="Skip zeros"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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." />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
317 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
318
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
319 <xml name="fragmentLength">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
320 <param argument="--fragmentLength" type="integer" value="300" min="1"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
321 label="Fragment length used for the sequencing"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
323 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
324
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
325 <xml name="scaleFactor">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
326 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
327 help="The computed scaling factor will be multiplied by this (default 1)." />
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
328 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
329
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
330 <xml name="scaleFactors">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
331 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
332 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
333 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
334
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
335 <xml name="stdio">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
336 <stdio>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
337 <exit_code range="1:" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
338 <exit_code range=":-1" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
339 <regex match="Error:" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
340 <regex match="Exception:" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
341 <regex match="EXception:" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
342 <regex match="Traceback" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
343 </stdio>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
344 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
345
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
346 <xml name="pseudocount">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
347 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
348 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
349
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
350 <token name="@REFERENCES@">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
351
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
352 .. class:: infomark
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
353
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
354 For more information on the tools, please visit our `help site`_.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
355
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
356 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
357
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
358 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
359
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
360 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
361 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
362 .. _help site: https://deeptools.readthedocs.org/
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
363
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
364 </token>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
365 <xml name="citations">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
366 <citations>
6
6a077ef72dd4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 5
diff changeset
367 <citation type="doi">10.1093/nar/gkw257</citation>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
368 <yield />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
369 </citations>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
370 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
371
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
372 <xml name="multiple_input_bams">
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
373 <conditional name="multibam_conditional">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
374 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
375 <option value="No" selected="true">No</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
376 <option value="Yes">Yes</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
377 </param>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
378 <when value="No">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
379 <param argument="--bamfiles" type="data" format="bam" min="1"
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
380 label="Bam file" multiple="true"
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
381 help=""/>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
382 </when>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
383 <when value="Yes">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
384 <repeat name="multibam_repeats" min="1" title="BAM Files">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
385 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
386 </repeat>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
387 </when>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
388 </conditional>
1
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
389 </xml>
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
390
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
391 <xml name="multiple_input_bams_min2">
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
392 <conditional name="multibam_conditional">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
393 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
394 is vital to you, select Yes below.">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
395 <option value="No" selected="true">No</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
396 <option value="Yes">Yes</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
397 </param>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
398 <when value="No">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
399 <param argument="--bamfiles" type="data" format="bam" min="2"
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
400 label="Bam file" multiple="true"
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
401 help=""/>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
402 </when>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
403 <when value="Yes">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
404 <repeat name="multibam_repeats" min="2" title="BAM Files">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
405 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
406 </repeat>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
407 </when>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
408 </conditional>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
409 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
410
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
411 <xml name="multiple_input_bigwigs">
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
412 <conditional name="multibigwig_conditional">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
413 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
414 is vital to you, select Yes below.">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
415 <option value="No" selected="true">No</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
416 <option value="Yes">Yes</option>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
417 </param>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
418 <when value="No">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
419 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
420 label="Bigwig file"
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
421 help="A Bigwig file."/>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
422 </when>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
423 <when value="Yes">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
424 <repeat name="multibigwig_repeats" min="2" title="BigWig files">
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
425 <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
426 </repeat>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
427 </when>
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
428 </conditional>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
429 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
430
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
431 <xml name="plotTitle">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
432 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
433 label="Title of the plot"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
434 help="Title of the plot, to be printed on top of the generated image." />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
435 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
436
1
edc6597ff21e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
437
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
438 <token name="@multiple_input_bams@">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
439 <![CDATA[
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
440 #set files=[]
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
441 #set labels=[]
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
442 #import re
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
443 #if $multibam_conditional.orderMatters == "No":
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
444 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
445 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
446 ln -s "${bamfile}" "./${counter}.bam" &&
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
448 #silent $files.append('%s.bam' % $counter)
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
449 #silent $labels.append("'%s'" % identifier)
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
450 #end for
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
451 #else:
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
453 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
11
4ae546bddd00 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
bgruening
parents: 10
diff changeset
454 ln -s "${f.bamfiles}" "./${counter}.bam" &&
4ae546bddd00 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
bgruening
parents: 10
diff changeset
455 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
456 #silent $files.append('%s.bam' % $counter)
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
457 #silent $labels.append("'%s'" % $identifier)
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
458 #end for
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
459 #end if
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
460 ]]>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
461 </token>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
462
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
463 <token name="@multiple_input_bigwigs@">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
464 <![CDATA[
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
465 #set files=[]
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
466 #set labels=[]
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
467 #import re
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
468 #if $multibigwig_conditional.orderMatters == "No":
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
469 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
470 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
471 ln -s "${bigwig}" "${counter}.bw" &&
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
472 #silent $files.append('%s.bw' % $counter)
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
473 #silent $labels.append("'%s'" % $identifier)
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
474 #end for
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
475 #else:
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
476 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
477 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
11
4ae546bddd00 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
bgruening
parents: 10
diff changeset
478 ln -s "${f.bigwigfiles}" "${counter}.bw" &&
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
479 #silent $files.append('%s.bw' % $counter)
12
94b05ea80203 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 11
diff changeset
480 #silent $labels.append("'%s'" % $identifier)
10
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
481 #end for
3317eb43a3c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 9
diff changeset
482 #end if
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
483 ]]>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
484 </token>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
485
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
486 <xml name="blacklist">
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
487 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
488 label="Blacklisted regions in BED/GTF format"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
489 help="One or more files containing regions to exclude from the analysis" />
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
490 </xml>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
491
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
492 <token name="@blacklist@">
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
493 <![CDATA[
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
494 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
495 #set blfiles=[]
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
496 #for $f in $advancedOpt.blackListFileName:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
497 #silent $blfiles.append("'%s'" % $f)
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
498 #end for
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
499 #if $blfiles != ["'None'"]:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
500 --blackListFileName #echo ' '.join($blfiles)#
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
501 #end if
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
502 #end if
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
503 ]]>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
504 </token>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
505
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
506 <xml name="multiple_bed">
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
507 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
508 label="Regions in BED/GTF format"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
509 help="One or more files containing regions to include in the analysis" />
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
510 </xml>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
511
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
512 <token name="@multiple_bed@">
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
513 <![CDATA[
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
514 #set files=[]
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
515 #set labels=[]
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
516 #for $f in $BED:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
517 #silent $files.append("'%s'" % $f)
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
518 #silent $labels.append("'%s'" % $f.display_name)
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
519 #end for
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
520 #if len($files) > 0:
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
521 --BED #echo ' '.join($files)#
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
522 --regionLabels #echo ' '.join($labels)#
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
523 #end if
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
524 ]]>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
525 </token>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
526
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
527 <xml name="reference_genome_source">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
528 <conditional name="source">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
529 <param name="ref_source" type="select" label="Reference genome">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
530 <option value="cached">locally cached</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
531 <option value="history">in your history</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
532 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
533 <when value="cached">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
534 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
535 <options from_data_table="lastz_seqs">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
536 <filter type="sort_by" column="1" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
537 <validator type="no_options" message="No indexes are available." />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
538 </options>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
539 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
540 </when>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
541 <when value="history">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
542 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
543 </when>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
544 </conditional>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
545 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
546
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
547 <token name="@reference_genome_source@">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
548 #if $source.ref_source=="history":
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
549 --genome $source.input1
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
550 #else:
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
551 --genome "$source.input1_2bit.fields.path"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
552 #end if
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
553 </token>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
554
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
555 <xml name="effectiveGenomeSize">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
556 <conditional name="effectiveGenomeSize">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
557 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
558 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
559 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
560 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
561 <option value="93260000">ce10 (93260000)</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
562 <option value="121400000">dm3 (121400000)</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
563 <option value="2451960000" selected="true">hg19 (2451960000)</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
564 <option value="2150570000">mm9 (2150570000)</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
565 <option value="specific">user specified</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
566 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
567 <when value="specific">
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
568 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
569 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
570 </when>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
571 <when value="2150570000" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
572 <when value="2451960000" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
573 <when value="121400000" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
574 <when value="93260000" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
575 </conditional>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
576 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
577
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
578 <xml name="skipNAs">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
579 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
580 label="Ignore missing data?"
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
581 help="This parameter determines if non-covered regions
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
582 (regions without overlapping reads) in a bam/bigWig file
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
583 should be skipped. The default is to treat those
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
584 regions as having a value of zero. The decision to
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
585 skip non-covered regions depends on the interpretation
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
586 of the data. Non-covered regions may represent, for
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
587 example, repetitive regions that should be ignored.
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
588 (default: False)" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
589 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
590
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
591 <xml name="input_save_matrix_values">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
592 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
593 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
594
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
595 <xml name="input_graphic_output_settings">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
596 <conditional name="output" >
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
597 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
598 <option value="no" selected="true">no</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
599 <option value="yes">yes</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
600 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
601 <when value="no" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
602 <when value="yes">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
603 <yield />
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
604 <param name="saveSortedRegions" type="boolean"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
605 label="Save the regions after skipping zeros or min/max threshold values"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
606 help="The order of the regions in the file follows the sorting order selected. This is useful,
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
607 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
608 </when>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
609 </conditional>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
610 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
611
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
612
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
613 <xml name="input_image_file_format">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
614 <param argument="--outFileFormat" type="select" label="Image file format">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
615 <option value="png" selected="true">png</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
616 <option value="pdf">pdf</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
617 <option value="svg">svg</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
618 <option value="eps">eps</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
619 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
620 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
621
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
622 <xml name="output_dpi">
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
623 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
624 label="Image dpi" help=""/>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
625 </xml>
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
626
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
627 <xml name="output_image_file_format">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
628 <data format="png" name="outFileName" label="${tool.name} image">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
629 <change_format>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
630 <when input="output.outFileFormat" value="pdf" format="pdf" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
631 <when input="output.outFileFormat" value="svg" format="svg" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
632 <when input="output.outFileFormat" value="eps" format="eps" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
633 </change_format>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
634 </data>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
635 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
636
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
637 <xml name="output_image_file_format_not_nested">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
638 <data format="png" name="outFileName" label="${tool.name} image">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
639 <change_format>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
640 <when input="outFileFormat" value="pdf" format="pdf" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
641 <when input="outFileFormat" value="svg" format="svg" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
642 <when input="outFileFormat" value="eps" format="eps" />
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
643 </change_format>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
644 </data>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
645 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
646
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
647 <xml name="output_save_matrix_values">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
648 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
649 <filter>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
650 ((
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
651 output['showOutputSettings'] == 'yes' and
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
652 output['saveMatrix'] is True
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
653 ))
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
654 </filter>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
655 </data>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
656 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
657
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
658 <xml name="output_graphic_outputs">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
659 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
660 <filter>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
661 ((
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
662 output['showOutputSettings'] == 'yes' and
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
663 output['saveSortedRegions'] is True
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
664 ))
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
665 </filter>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
666 </data>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
667 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
668
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
669 <xml name="colorMap">
8
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
670 <param name="colorMap" type="select" label="Color map to use for the heatmap"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
671 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
6fc072c36dc9 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents: 7
diff changeset
672 multiple="true">
0
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
673 <option value="RdYlBu" selected="true">RdYlBu</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
674 <option value="Accent">Accent</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
675 <option value="Spectral">Spectral</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
676 <option value="Set1">Set1</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
677 <option value="Set2">Set2</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
678 <option value="Set3">Set3</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
679 <option value="Dark2">Dark2</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
680 <option value="Reds">Reds</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
681 <option value="Oranges">Oranges</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
682 <option value="Greens">Greens</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
683 <option value="Blues">Blues</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
684 <option value="Greys">Greys</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
685 <option value="Purples">Purples</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
686 <option value="Paired">Paired</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
687 <option value="Pastel1">Pastel1</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
688 <option value="Pastel2">Pastel2</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
689 <option value="spring">spring</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
690 <option value="summer">summer</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
691 <option value="autumn">autumn</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
692 <option value="winter">winter</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
693 <option value="hot">hot</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
694 <option value="coolwarm">coolwarm</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
695 <option value="cool">cool</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
696 <option value="seismic">seismic</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
697 <option value="terrain">terrain</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
698 <option value="ocean">ocean</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
699 <option value="rainbow">rainbow</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
700 <option value="bone">bone</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
701 <option value="flag">flag</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
702 <option value="prism">prism</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
703 <option value="cubehelix">cubehelix</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
704 <option value="binary">binary</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
705 <option value="pink">pink</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
706 <option value="gray">gray</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
707 <option value="copper">copper</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
708 <option value="BrBG">BrBG</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
709 <option value="BuGn">BuGn</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
710 <option value="BuPu">BuPu</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
711 <option value="GnBu">GnBu</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
712 <option value="OrRd">OrRd</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
713 <option value="PiYG">PiYG</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
714 <option value="PRGn">PRGn</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
715 <option value="PuOr">PuOr</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
716 <option value="PuRd">PuRd</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
717 <option value="PuBu">PuBu</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
718 <option value="RdBu">RdBu</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
719 <option value="RdGy">RdGy</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
720 <option value="RdPu">RdPu</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
721 <option value="YlGn">YlGn</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
722 <option value="PuBuGn">PuBuGn</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
723 <option value="RdYlGn">RdYlGn</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
724 <option value="YlGnBu">YlGnBu</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
725 <option value="YlOrBr">YlOrBr</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
726 <option value="YlOrRd">YlOrRd</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
727 <option value="gist_gray">gist_gray</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
728 <option value="gist_stern">gist_stern</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
729 <option value="gist_earth">gist_earth</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
730 <option value="gist_yarg">gist_yarg</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
731 <option value="gist_ncar">gist_ncar</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
732 <option value="gist_rainbow">gist_rainbow</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
733 <option value="gist_heat">gist_heat</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
734 <option value="gnuplot">gnuplot</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
735 <option value="gnuplot2">gnuplot2</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
736 <option value="CMRmap">CMRmap</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
737 <option value="bwr">bwr</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
738 <option value="hsv">hsv</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
739 <option value="brg">brg</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
740 <option value="jet">jet</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
741 <option value="afmhot">afmhot</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
742 <option value="Accent_r">Accent reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
743 <option value="Spectral_r">Spectral reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
744 <option value="Set1_r">Set1 reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
745 <option value="Set2_r">Set2 reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
746 <option value="Set3_r">Set3 reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
747 <option value="Dark2_r">Dark2 reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
748 <option value="Reds_r">Reds reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
749 <option value="Oranges_r">Oranges reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
750 <option value="Greens_r">Greens reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
751 <option value="Blues_r">Blues reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
752 <option value="Greys_r">Greys reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
753 <option value="Purples_r">Purples reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
754 <option value="Paired_r">Paired reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
755 <option value="Pastel1_r">Pastel1 reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
756 <option value="Pastel2_r">Pastel2 reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
757 <option value="spring_r">spring reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
758 <option value="summer_r">summer reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
759 <option value="autumn_r">autumn reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
760 <option value="winter_r">winter reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
761 <option value="hot_r">hot reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
762 <option value="coolwarm_r">coolwarm reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
763 <option value="cool_r">cool reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
764 <option value="seismic_r">seismic reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
765 <option value="terrain_r">terrain reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
766 <option value="ocean_r">ocean reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
767 <option value="rainbow_r">rainbow reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
768 <option value="bone_r">bone reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
769 <option value="flag_r">flag reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
770 <option value="prism_r">prism reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
771 <option value="cubehelix_r">cubehelix reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
772 <option value="binary_r">binary reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
773 <option value="pink_r">pink reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
774 <option value="gray_r">gray reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
775 <option value="copper_r">copper reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
776 <option value="BrBG_r">BrBG reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
777 <option value="BuGn_r">BuGn reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
778 <option value="BuPu_r">BuPu reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
779 <option value="GnBu_r">GnBu reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
780 <option value="OrRd_r">OrRd reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
781 <option value="PiYG_r">PiYG reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
782 <option value="PRGn_r">PRGn reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
783 <option value="PuOr_r">PuOr reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
784 <option value="PuRd_r">PuRd reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
785 <option value="PuBu_r">PuBu reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
786 <option value="RdBu_r">RdBu reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
787 <option value="RdGy_r">RdGy reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
788 <option value="RdPu_r">RdPu reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
789 <option value="YlGn_r">YlGn reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
790 <option value="PuBuGn_r">PuBuGn reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
791 <option value="RdYlBu_r">RdYlBu reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
792 <option value="RdYlGn_r">RdYlGn reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
793 <option value="YlGnBu_r">YlGnBu reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
794 <option value="YlOrBr_r">YlOrBr reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
795 <option value="YlOrRd_r">YlOrRd reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
796 <option value="gist_gray_r">gist_gray reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
797 <option value="gist_stern_r">gist_stern reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
798 <option value="gist_earth_r">gist_earth reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
799 <option value="gist_yarg_r">gist_yarg reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
800 <option value="gist_ncar_r">gist_ncar reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
801 <option value="gist_rainbow_r">gist_rainbow reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
802 <option value="gist_heat_r">gist_heat reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
803 <option value="gnuplot_r">gnuplot reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
804 <option value="gnuplot2_r">gnuplot2 reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
805 <option value="CMRmap_r">CMRmap reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
806 <option value="bwr_r">bwr reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
807 <option value="hsv_r">hsv reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
808 <option value="brg_r">brg reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
809 <option value="jet_r">jet reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
810 <option value="afmhot_r">afmhot reversed</option>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
811 </param>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
812
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
813 </xml>
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
814
268ab1ca4091 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
815 </macros>