Mercurial > repos > bgruening > deeptools_plot_pca
annotate deepTools_macros.xml @ 18:197e568bdc13 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356
author | bgruening |
---|---|
date | Fri, 18 Mar 2016 08:36:33 -0400 |
parents | 179b2441ae0b |
children | 924d3e517c0d |
rev | line source |
---|---|
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
1 <macros> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
2 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
3 <xml name="advancedOpt_scaffold"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
4 <conditional name="advancedOpt"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
5 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
6 <option value="no" selected="true">no</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
7 <option value="yes">yes</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
8 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
9 <when value="no" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
10 <when value="yes"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
11 <yield/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
12 </when> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
13 </conditional> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
14 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
15 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
16 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
17 #if $advancedOpt.doExtendCustom.doExtend == 'custom': |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes': |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
20 --extendReads |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
21 #end if |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
22 $advancedOpt.ignoreDuplicates |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
23 $advancedOpt.centerReads |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
24 #if $advancedOpt.minMappingQuality: |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
25 --minMappingQuality '$advancedOpt.minMappingQuality' |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
26 #end if |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
27 #if $advancedOpt.samFlagInclude: |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
28 --samFlagInclude $advancedOpt.samFlagInclude |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
29 #end if |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
30 #if $advancedOpt.samFlagExclude: |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
31 --samFlagExclude $advancedOpt.samFlagExclude |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
32 #end if |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
33 </token> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
34 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
35 <xml name="heatmap_options"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
36 <expand macro="zMin_zMax" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
37 <expand macro="colorMap" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
38 <expand macro="plotTitle" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
39 <expand macro="plotNumbers" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
40 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
41 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
42 <token name="@HEATMAP_OPTIONS@"> |
7
4bd03b1a8da7
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69
bgruening
parents:
6
diff
changeset
|
43 #if str($plotting_type.zMin) != "": |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
44 --zMin $plotting_type.zMin |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
45 #end if |
7
4bd03b1a8da7
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69
bgruening
parents:
6
diff
changeset
|
46 #if str($plotting_type.zMax) != "": |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
47 --zMax $plotting_type.zMax |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
48 #end if |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
49 --colorMap '$plotting_type.colorMap' |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
50 $plotting_type.plotNumbers |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
51 --plotTitle '$plotting_type.plotTitle' |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
52 </token> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
53 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
54 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
55 <xml name="includeZeros"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
57 label="Include zeros" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
58 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." /> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
59 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
60 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
61 <xml name="zMin_zMax"> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities" |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
63 help="If not specified the value is set automatically."/> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities" |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
65 help="If not specified the value is set automatically."/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
66 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
67 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
68 <xml name="region_limit_operation"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
69 <param argument="--region" type="text" value="" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
70 label="Region of the genome to limit the operation to" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
71 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
72 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
73 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
16
179b2441ae0b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
bgruening
parents:
14
diff
changeset
|
75 <token name="@WRAPPER_VERSION@">2.2.2</token> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
76 <xml name="requirements"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
77 <requirements> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
78 <requirement type="package" version="2.7.10">python</requirement> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
79 <requirement type="binary">@BINARY@</requirement> |
16
179b2441ae0b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
bgruening
parents:
14
diff
changeset
|
80 <requirement type="package" version="2.2.2">deepTools</requirement> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
81 <yield /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
82 </requirements> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
83 <expand macro="stdio" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
84 <version_command>@BINARY@ --version</version_command> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
85 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
86 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
87 <xml name="smoothLength"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
88 <param argument="--smoothLength" type="integer" value="" optional="True" min="1" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
89 label="Smooth values using the following length (in bases)" |
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
90 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
91 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
92 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
93 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
94 <xml name="kmeans_clustering"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
95 <conditional name="used_multiple_regions"> |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
96 <param name="used_multiple_regions_options" type="select" |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
97 label="Did you compute the matrix with more than one groups of regions?" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
98 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
99 <option value="yes">Yes, I used multiple groups of regions</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
100 <option value="no">No, I used only one group</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
101 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
102 <when value="no"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
103 <conditional name="clustering"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
104 <param name="clustering_options" type="select" label="Clustering algorithm"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
105 <option value="none">No clustering</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
106 <option value="kmeans">Kmeans clustering</option> |
13
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
107 <option value="hclust">Hierarchical clustering</option> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
108 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
109 <when value="kmeans"> |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
110 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
111 help="When this option is set, the matrix is split into clusters using the k-means algorithm. |
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
112 This only works for data that is not grouped, otherwise only the first group will be clustered. |
7
4bd03b1a8da7
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69
bgruening
parents:
6
diff
changeset
|
113 If more specific clustering methods are required it is advisable to save the underlying matrix and |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
114 run the clustering using other software."/> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
115 </when> |
13
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
116 <when value="hclust"> |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
117 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
118 help="WARNING: This option causes the tool to run for a very long time! When this option is |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
119 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
120 This only works for data that is not grouped, otherwise only the first group will be clustered. |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
121 Note that you must have used the '--missingDataAsZero' option within computeMatrix! |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
122 If more specific clustering methods are required it is advisable to save the underlying matrix and |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
123 run the clustering using other software."/> |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
124 </when> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
125 <when value="none" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
126 </conditional> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
127 </when> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
128 <when value="yes" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
129 </conditional> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
130 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
131 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
132 <token name="@KMEANS_CLUSTERING@"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
133 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
134 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
135 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
136 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
137 #end if |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
138 #end if |
13
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
139 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
140 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
141 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
142 #end if |
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
143 #end if |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
144 #end if |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
145 </token> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
146 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
147 <xml name="samFlags"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
148 <param argument="--samFlagInclude" type="integer" optional="True" value="" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
149 label="Include reads based on the SAM flag" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
150 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."/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
151 <param argument="--samFlagExclude" type="integer" optional="True" value="" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
152 label="Exclude reads based on the SAM flag" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
153 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."/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
154 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
155 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
156 <xml name="read_processing_options"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
157 <expand macro="extendReads" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
158 <expand macro="ignoreDuplicates" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
159 <expand macro="centerReads" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
160 <expand macro="minMappingQuality" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
161 <expand macro="samFlags" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
162 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
163 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
164 <xml name="plotNumbers"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
165 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
166 label="Plot the correlation value" |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
167 help="If set, then the correlation number is plotted on top of the heatmap."/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
168 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
169 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
170 <xml name="extendReads"> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
171 <conditional name="doExtendCustom"> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
172 <param name="doExtend" type="select" label="Extend reads to the given average fragment size." |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
173 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here. |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
174 By default *each* read mate is extended. |
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
175 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. |
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
176 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. |
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
177 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 |
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
178 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
179 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
180 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
181 <option value="custom">A custom length, which will be applied to ALL reads.</option> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
182 </param> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
183 <when value="no" /> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
184 <when value="yes" /> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
185 <when value="custom"> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
186 <param name="extendReadsValue" type="integer" value="300" min="1" |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
187 label="Extend reads to the given average fragment size" |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
188 help="Extend all reads to this length" /> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
189 </when> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
190 </conditional> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
191 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
192 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
193 <xml name="corMethod"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
194 <param argument="--corMethod" type="select" label="Correlation method"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
195 <option value="spearman" selected="True">Spearman</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
196 <option value="pearson">Pearson</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
197 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
198 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
199 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
200 <xml name="distanceBetweenBins"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
201 <param argument="--distanceBetweenBins" type="integer" value="0" min="0" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
202 label="Distance between bins" |
11
f173cc2d28f9
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
9
diff
changeset
|
203 help="By default, multiBamSummary considers consecutive bins of |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
204 the specified 'Bin size'. However, to reduce the |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
205 computation time, a larger distance between bins can |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
206 be given. Larger distances result in fewer bins being |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
207 considered."/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
208 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
209 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
210 <xml name="centerReads"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
211 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
212 label="Center regions with respect to the fragment length" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
213 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
214 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
215 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
216 <xml name="ignoreDuplicates"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
217 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
218 label="Ignore duplicates" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
219 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." /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
220 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
221 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
222 <xml name="sortUsing"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
223 <param argument="--sortUsing" type="select" label="Method used for sorting" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
224 help="For each row the method is computed."> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
225 <option value="mean" selected="true">mean</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
226 <option value="median">median</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
227 <option value="min">min</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
228 <option value="max">max</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
229 <option value="sum">sum</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
230 <option value="region_length">region length</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
231 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
232 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
233 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
234 <xml name="sortRegions"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
235 <param argument="--sortRegions" type="select" label="Sort regions" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
236 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
237 <option value="no">no ordering</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
238 <option value="descend" selected="true">descending order</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
239 <option value="ascend">ascending order</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
240 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
241 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
242 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
243 <xml name="minMappingQuality"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
244 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
245 label="Minimum mapping quality" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
246 help= "If set, only reads with a mapping quality score higher than this value are considered."/> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
247 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
248 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
249 <xml name="skipZeros"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
250 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
251 label ="Skip zeros" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
252 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." /> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
253 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
254 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
255 <xml name="fragmentLength"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
256 <param argument="--fragmentLength" type="integer" value="300" min="1" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
257 label="Fragment length used for the sequencing" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
258 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
259 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
260 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
261 <xml name="scaleFactor"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
262 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
263 help="When used in combination with --normalizeTo1x or |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
264 --normalizeUsingRPKM, the computed scaling factor will |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
265 be multiplied by the given scale factor." /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
266 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
267 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
268 <xml name="scaleFactors"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
269 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
270 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
271 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
272 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
273 <xml name="stdio"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
274 <stdio> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
275 <exit_code range="1:" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
276 <exit_code range=":-1" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
277 <regex match="Error:" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
278 <regex match="Exception:" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
279 <regex match="EXception:" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
280 <regex match="Traceback" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
281 </stdio> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
282 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
283 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
284 <xml name="pseudocount"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
285 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
286 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
287 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
288 <token name="@REFERENCES@"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
289 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
290 .. class:: infomark |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
291 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
292 For more information on the tools, please visit our `help site`_. |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
293 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
294 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
295 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
296 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
297 |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
298 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
299 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
300 .. _help site: https://deeptools.readthedocs.org/ |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
301 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
302 </token> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
303 <xml name="citations"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
304 <citations> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
305 <citation type="doi">10.1093/nar/gku365</citation> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
306 <yield /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
307 </citations> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
308 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
309 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
310 <xml name="multiple_input_bams"> |
14
4477ae4c026d
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
13
diff
changeset
|
311 <param argument="--bamfiles" type="data" format="bam" min="1" |
4477ae4c026d
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
13
diff
changeset
|
312 label="Bam file" multiple="true" |
16
179b2441ae0b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
bgruening
parents:
14
diff
changeset
|
313 help=""/> |
14
4477ae4c026d
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
13
diff
changeset
|
314 </xml> |
4477ae4c026d
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
13
diff
changeset
|
315 |
4477ae4c026d
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
13
diff
changeset
|
316 <xml name="multiple_input_bams_min2"> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
317 <param argument="--bamfiles" type="data" format="bam" min="2" |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
318 label="Bam file" multiple="true" |
16
179b2441ae0b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
bgruening
parents:
14
diff
changeset
|
319 help=""/> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
320 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
321 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
322 <xml name="multiple_input_bigwigs"> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
323 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
324 label="Bigwig file" |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
325 help="A Bigwig file."/> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
326 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
327 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
328 <xml name="plotTitle"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
329 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
330 label="Title of the plot" |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
331 help="Title of the plot, to be printed on top of the generated image." /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
332 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
333 |
13
0a198e327cc1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
12
diff
changeset
|
334 |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
335 <token name="@multiple_input_bams@"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
336 <![CDATA[ |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
337 #set files=[] |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
338 #set labels=[] |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
339 #for $counter, $bamfile in enumerate($bamfiles): |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
340 ln -s "${bamfile}" "./${counter}.bam" && |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
341 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
342 #silent $files.append('%s.bam' % $counter) |
18
197e568bdc13
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356
bgruening
parents:
16
diff
changeset
|
343 #silent $labels.append("'%s'" % ($bamfile.display_name)) |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
344 #end for |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
345 ]]> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
346 </token> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
347 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
348 <token name="@multiple_input_bigwigs@"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
349 <![CDATA[ |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
350 #set files=[] |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
351 #set labels=[] |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
352 #for $counter, $bigwig in enumerate($bigwigfiles): |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
353 ln -s "${bigwig}" "${counter}.bw" && |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
354 #silent $files.append('%s.bw' % $counter) |
18
197e568bdc13
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356
bgruening
parents:
16
diff
changeset
|
355 #silent $labels.append("'%s'" % ($bigwig.display_name)) |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
356 #end for |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
357 ]]> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
358 </token> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
359 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
360 <xml name="reference_genome_source"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
361 <conditional name="source"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
362 <param name="ref_source" type="select" label="Reference genome"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
363 <option value="cached">locally cached</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
364 <option value="history">in your history</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
365 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
366 <when value="cached"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
367 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
368 <options from_data_table="lastz_seqs"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
369 <filter type="sort_by" column="1" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
370 <validator type="no_options" message="No indexes are available." /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
371 </options> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
372 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
373 </when> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
374 <when value="history"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
375 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
376 </when> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
377 </conditional> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
378 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
379 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
380 <token name="@reference_genome_source@"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
381 #if $source.ref_source=="history": |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
382 --genome $source.input1 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
383 #else: |
4
cc4f39428bdf
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
bgruening
parents:
3
diff
changeset
|
384 --genome "$source.input1_2bit.fields.path" |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
385 #end if |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
386 </token> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
387 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
388 <xml name="effectiveGenomeSize"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
389 <conditional name="effectiveGenomeSize"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
390 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
391 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. |
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
392 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
393 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."> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
394 <option value="93260000">ce10 (93260000)</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
395 <option value="121400000">dm3 (121400000)</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
396 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
397 <option value="2150570000">mm9 (2150570000)</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
398 <option value="specific">user specified</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
399 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
400 <when value="specific"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
401 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
402 </when> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
403 <when value="2150570000" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
404 <when value="2451960000" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
405 <when value="121400000" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
406 <when value="93260000" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
407 </conditional> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
408 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
409 |
1
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
410 <xml name="skipNAs"> |
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
411 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" |
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
412 label="Ignore missing data?" |
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
413 help="This parameter determines if non-covered regions |
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
414 (regions without overlapping reads) in a bam/bigWig file |
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
415 should be skipped. The default is to treat those |
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
416 regions as having a value of zero. The decision to |
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
417 skip non-covered regions depends on the interpretation |
8
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
418 of the data. Non-covered regions may represent, for |
c74dd623b281
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
bgruening
parents:
7
diff
changeset
|
419 example, repetitive regions that should be ignored. |
1
439451971446
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
bgruening
parents:
0
diff
changeset
|
420 (default: False)" /> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
421 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
422 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
423 <xml name="input_save_matrix_values"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
424 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
425 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
426 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
427 <xml name="input_graphic_output_settings"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
428 <conditional name="output" > |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
429 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
430 <option value="no" selected="true">no</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
431 <option value="yes">yes</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
432 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
433 <when value="no" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
434 <when value="yes"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
435 <yield /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
436 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
437 </when> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
438 </conditional> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
439 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
440 |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
441 |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
442 <xml name="input_image_file_format"> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
443 <param argument="--outFileFormat" type="select" label="Image file format"> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
444 <option value="png" selected="true">png</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
445 <option value="pdf">pdf</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
446 <option value="svg">svg</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
447 <option value="eps">eps</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
448 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
449 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
450 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
451 <xml name="output_image_file_format"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
452 <data format="png" name="outFileName" label="${tool.name} image"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
453 <change_format> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
454 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
455 <when input="output.outFileFormat" value="svg" format="svg" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
456 <when input="output.outFileFormat" value="eps" format="eps" /> |
3
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
457 </change_format> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
458 </data> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
459 </xml> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
460 |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
461 <xml name="output_image_file_format_not_nested"> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
462 <data format="png" name="outFileName" label="${tool.name} image"> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
463 <change_format> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
464 <when input="outFileFormat" value="pdf" format="pdf" /> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
465 <when input="outFileFormat" value="svg" format="svg" /> |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
bgruening
parents:
2
diff
changeset
|
466 <when input="outFileFormat" value="eps" format="eps" /> |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
467 </change_format> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
468 </data> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
469 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
470 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
471 <xml name="output_save_matrix_values"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
472 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
473 <filter> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
474 (( |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
475 output['showOutputSettings'] == 'yes' and |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
476 output['saveMatrix'] is True |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
477 )) |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
478 </filter> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
479 </data> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
480 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
481 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
482 <xml name="output_graphic_outputs"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
483 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
484 <filter> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
485 (( |
2
828ecc09ca38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
bgruening
parents:
1
diff
changeset
|
486 output['showOutputSettings'] == 'yes' and |
0
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
487 output['saveSortedRegions'] is True |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
488 )) |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
489 </filter> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
490 </data> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
491 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
492 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
493 <xml name="colorMap"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
494 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
495 <option value="RdYlBu" selected="true">RdYlBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
496 <option value="Accent">Accent</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
497 <option value="Spectral">Spectral</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
498 <option value="Set1">Set1</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
499 <option value="Set2">Set2</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
500 <option value="Set3">Set3</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
501 <option value="Dark2">Dark2</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
502 <option value="Reds">Reds</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
503 <option value="Oranges">Oranges</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
504 <option value="Greens">Greens</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
505 <option value="Blues">Blues</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
506 <option value="Greys">Greys</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
507 <option value="Purples">Purples</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
508 <option value="Paired">Paired</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
509 <option value="Pastel1">Pastel1</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
510 <option value="Pastel2">Pastel2</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
511 <option value="spring">spring</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
512 <option value="summer">summer</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
513 <option value="autumn">autumn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
514 <option value="winter">winter</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
515 <option value="hot">hot</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
516 <option value="coolwarm">coolwarm</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
517 <option value="cool">cool</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
518 <option value="seismic">seismic</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
519 <option value="terrain">terrain</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
520 <option value="ocean">ocean</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
521 <option value="rainbow">rainbow</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
522 <option value="bone">bone</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
523 <option value="flag">flag</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
524 <option value="prism">prism</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
525 <option value="cubehelix">cubehelix</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
526 <option value="binary">binary</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
527 <option value="pink">pink</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
528 <option value="gray">gray</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
529 <option value="copper">copper</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
530 <option value="BrBG">BrBG</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
531 <option value="BuGn">BuGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
532 <option value="BuPu">BuPu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
533 <option value="GnBu">GnBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
534 <option value="OrRd">OrRd</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
535 <option value="PiYG">PiYG</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
536 <option value="PRGn">PRGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
537 <option value="PuOr">PuOr</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
538 <option value="PuRd">PuRd</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
539 <option value="PuBu">PuBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
540 <option value="RdBu">RdBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
541 <option value="RdGy">RdGy</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
542 <option value="RdPu">RdPu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
543 <option value="YlGn">YlGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
544 <option value="PuBuGn">PuBuGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
545 <option value="RdYlGn">RdYlGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
546 <option value="YlGnBu">YlGnBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
547 <option value="YlOrBr">YlOrBr</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
548 <option value="YlOrRd">YlOrRd</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
549 <option value="gist_gray">gist_gray</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
550 <option value="gist_stern">gist_stern</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
551 <option value="gist_earth">gist_earth</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
552 <option value="gist_yarg">gist_yarg</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
553 <option value="gist_ncar">gist_ncar</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
554 <option value="gist_rainbow">gist_rainbow</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
555 <option value="gist_heat">gist_heat</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
556 <option value="gnuplot">gnuplot</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
557 <option value="gnuplot2">gnuplot2</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
558 <option value="CMRmap">CMRmap</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
559 <option value="bwr">bwr</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
560 <option value="hsv">hsv</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
561 <option value="brg">brg</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
562 <option value="jet">jet</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
563 <option value="afmhot">afmhot</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
564 <option value="Accent_r">Accent reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
565 <option value="Spectral_r">Spectral reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
566 <option value="Set1_r">Set1 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
567 <option value="Set2_r">Set2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
568 <option value="Set3_r">Set3 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
569 <option value="Dark2_r">Dark2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
570 <option value="Reds_r">Reds reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
571 <option value="Oranges_r">Oranges reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
572 <option value="Greens_r">Greens reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
573 <option value="Blues_r">Blues reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
574 <option value="Greys_r">Greys reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
575 <option value="Purples_r">Purples reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
576 <option value="Paired_r">Paired reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
577 <option value="Pastel1_r">Pastel1 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
578 <option value="Pastel2_r">Pastel2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
579 <option value="spring_r">spring reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
580 <option value="summer_r">summer reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
581 <option value="autumn_r">autumn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
582 <option value="winter_r">winter reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
583 <option value="hot_r">hot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
584 <option value="coolwarm_r">coolwarm reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
585 <option value="cool_r">cool reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
586 <option value="seismic_r">seismic reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
587 <option value="terrain_r">terrain reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
588 <option value="ocean_r">ocean reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
589 <option value="rainbow_r">rainbow reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
590 <option value="bone_r">bone reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
591 <option value="flag_r">flag reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
592 <option value="prism_r">prism reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
593 <option value="cubehelix_r">cubehelix reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
594 <option value="binary_r">binary reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
595 <option value="pink_r">pink reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
596 <option value="gray_r">gray reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
597 <option value="copper_r">copper reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
598 <option value="BrBG_r">BrBG reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
599 <option value="BuGn_r">BuGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
600 <option value="BuPu_r">BuPu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
601 <option value="GnBu_r">GnBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
602 <option value="OrRd_r">OrRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
603 <option value="PiYG_r">PiYG reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
604 <option value="PRGn_r">PRGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
605 <option value="PuOr_r">PuOr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
606 <option value="PuRd_r">PuRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
607 <option value="PuBu_r">PuBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
608 <option value="RdBu_r">RdBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
609 <option value="RdGy_r">RdGy reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
610 <option value="RdPu_r">RdPu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
611 <option value="YlGn_r">YlGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
612 <option value="PuBuGn_r">PuBuGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
613 <option value="RdYlBu_r">RdYlBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
614 <option value="RdYlGn_r">RdYlGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
615 <option value="YlGnBu_r">YlGnBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
616 <option value="YlOrBr_r">YlOrBr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
617 <option value="YlOrRd_r">YlOrRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
618 <option value="gist_gray_r">gist_gray reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
619 <option value="gist_stern_r">gist_stern reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
620 <option value="gist_earth_r">gist_earth reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
621 <option value="gist_yarg_r">gist_yarg reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
622 <option value="gist_ncar_r">gist_ncar reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
623 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
624 <option value="gist_heat_r">gist_heat reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
625 <option value="gnuplot_r">gnuplot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
626 <option value="gnuplot2_r">gnuplot2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
627 <option value="CMRmap_r">CMRmap reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
628 <option value="bwr_r">bwr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
629 <option value="hsv_r">hsv reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
630 <option value="brg_r">brg reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
631 <option value="jet_r">jet reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
632 <option value="afmhot_r">afmhot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
633 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
634 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
635 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
636 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
637 </macros> |