Mercurial > repos > bgruening > deeptools_plot_heatmap

annotate plotHeatmap.xml @ 7:e57bfadcab30 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3ea8716dd65a9abde96b69610be31571e4f0ae6d
author bgruening
date Fri, 13 May 2016 14:03:24 -0400
parents 6a247ae015cc
children ca218dae7902
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0">
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
2 <description>creates a heatmap for score distributions across genomic regions</description>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
3 <macros>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
4 <token name="@BINARY@">plotHeatmap</token>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
5 <import>deepTools_macros.xml</import>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
6 </macros>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
7 <expand macro="requirements"/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
8 <command>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
9 <![CDATA[
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
10 @BINARY@
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
11 --matrixFile "$matrixFile"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
12 --outFileName "$outFileName"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
13
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
14 #if $output.showOutputSettings == "yes"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
15 --plotFileFormat "$output.outFileFormat"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
16
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
17 #if $outFileNameMatrix:
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
18 --outFileNameMatrix "$outFileNameMatrix"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
19 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
20
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
21 #if $outFileSortedRegions:
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
22 --outFileSortedRegions "$outFileSortedRegions"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
23 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
24 #else
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
25 --plotFileFormat 'png'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
26 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
27
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
28 #if $advancedOpt.showAdvancedOpt == "yes"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
29 #if $advancedOpt.sortRegions:
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
30 --sortRegions '$advancedOpt.sortRegions'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
31 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
32
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
33 #if $advancedOpt.sortUsing:
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
34 --sortUsing '$advancedOpt.sortUsing'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
35 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
36
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
37 #if $advancedOpt.averageTypeSummaryPlot:
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
38 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
39 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
40
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
41 #if str($advancedOpt.missingDataColor.value) != "None":
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
42 --missingDataColor '$advancedOpt.missingDataColor'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
43 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
44
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
45 --colorMap '$advancedOpt.colorMap'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
46
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
47 #if str($advancedOpt.zMin).strip() != "":
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
48 --zMin $advancedOpt.zMin
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
49 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
50 #if $advancedOpt.zMax:
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
51 --zMax $advancedOpt.zMax
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
52 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
53
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
54 #if str($advancedOpt.yMin).strip() != "":
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
55 --yMin $advancedOpt.yMin
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
56 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
57 #if $advancedOpt.yMax:
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
58 --yMax $advancedOpt.yMax
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
59 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
60
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
61 --xAxisLabel '$advancedOpt.xAxisLabel'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
62 --yAxisLabel '$advancedOpt.yAxisLabel'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
63
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
64 --heatmapWidth $advancedOpt.heatmapWidth
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
65 --heatmapHeight $advancedOpt.heatmapHeight
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
66
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
67 --whatToShow '$advancedOpt.whatToShow'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
68
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
69 --startLabel '$advancedOpt.startLabel'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
70 --endLabel '$advancedOpt.endLabel'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
71
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
72 --refPointLabel '$advancedOpt.referencePointLabel'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
73
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
74 #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
75 --samplesLabel $advancedOpt.samplesLabel
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
76 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
77
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
78 #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
79 --regionsLabel $advancedOpt.regionsLabel
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
80 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
81
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
82 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
83 --plotTitle '$advancedOpt.plotTitle'
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
84 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
85
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
86 $advancedOpt.perGroup
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
87
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
88 @KMEANS_CLUSTERING@
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
89
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
90 #end if
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
91 ]]>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
92 </command>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
93 <inputs>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
94 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
95
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
96 <expand macro="input_graphic_output_settings">
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
97 <expand macro="input_image_file_format" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
98 <expand macro="input_save_matrix_values" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
99 </expand>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
100
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
101 <conditional name="advancedOpt" >
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
102 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
103 <option value="no" selected="true">no</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
104 <option value="yes">yes</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
105 </param>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
106 <when value="no" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
107 <when value="yes">
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
108 <expand macro="sortRegions" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
109 <expand macro="sortUsing" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
110 <param argument="--averageTypeSummaryPlot" type="select"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
111 label="Type of statistic that should be plotted in the summary image above the heatmap"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
112 help="">
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
113 <option value="mean" selected="true">mean</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
114 <option value="median">median</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
115 <option value="min">min</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
116 <option value="max">max</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
117 <option value="sum">sum</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
118 <option value="std">std</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
119 </param>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
120
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
121 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
122 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
123 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
124 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
125 Alternatively colors can be specified using the #rrggbb notation." />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
126
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
127 <expand macro="colorMap" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
128
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
129 <param argument="--zMin" type="float" value="" size="3" optional="True"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
130 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help=""/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
131 <param argument="--zMax" type="float" value="" size="3" optional="True"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
132 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help=""/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
133 <param argument="--yMin" type="float" value="" size="3" optional="True"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
134 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
135 <param argument="--yMax" type="float" value="" size="3" optional="True"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
136 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
137 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
138 label="The x-axis label" help="" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
139 <param argument="--yAxisLabel" type="text" value="genes" size="30"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
140 label="The y-axis label for the top panel" help="" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
141
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
142 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
143 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
144 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
145 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
146
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
147 <param argument="--whatToShow" type="select" label="What to show"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
148 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
149 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
150 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
151 <option value="heatmap and colorbar">heatmap and colorbar</option>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
152 </param>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
153
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
154 <param argument="--startLabel" type="text" value="TSS" size="10"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
155 label="Label for the region start"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
156 help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
157 <param argument="--endLabel" type="text" value="TES" size="10"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
158 label="Label for the region end"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
159 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
160
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
161 <param argument="--referencePointLabel" type="text" value="TSS" size="10"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
162 label="Reference point label"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
163 help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
164 <param argument="--samplesLabel" type="text" size="30"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
165 label="Labels for the samples (each bigwig) plotted"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
166 help="The default is to use the file name of the sample. The sample labels should be separated by
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
167 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
168 <sanitizer>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
169 <valid initial="string.printable">
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
170 </valid>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
171 </sanitizer>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
172 </param>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
173 <param argument="--regionsLabel" type="text" size="30"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
174 label="Labels for the regions plotted in the heatmap"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
175 help="If more than one region is being plotted a list of labels separated by space is required.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
176 If a label itself contains a space, then quotes are needed.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
177 For example, label_1, &quot;label 2&quot;" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
178
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
179 <expand macro="plotTitle" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
180 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
181 label="Make one plot per group of regions"
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
182 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
183
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
184 <expand macro="kmeans_clustering" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
185 </when>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
186 </conditional>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
187 </inputs>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
188 <outputs>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
189 <expand macro="output_image_file_format" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
190 <expand macro="output_graphic_outputs" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
191 <expand macro="output_save_matrix_values" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
192 </outputs>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
193 <tests>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
194 <test>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
195 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
196 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
197 </test>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
198 <test>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
199 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
200 <param name="showAdvancedOpt" value="yes" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
201 <param name="whatToShow" value="heatmap and colorbar" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
202 <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
203 </test>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
204 </tests>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
205 <help>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
206 <![CDATA[
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
207
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
208 What it does
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
209 --------------
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
210
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
211 ``plotHeatmap`` visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
212 Like ``plotProfile``, it requires that computeMatrix was run first to calculate the values.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
213
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
214 We have implemented a number of optional parameters to optimize the visual output and we encourage you to play around with the min/max values
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
215 displayed in the heatmap as well as with the different coloring options.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
216
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
217 **TIP:** *If your data is rather sparse and the resulting heatmap is too black, change the "Missing data color" to white (via "Advanced options").*
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
218
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
219 The most powerful option is probably the **k-means/hierarchical clustering** where you can sort your regions into groups of regions with similar score distributions.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
220
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
221 **NOTE:** *The clustering will only work if you supplied a single BED file to computeMatrix. plotHeatmap cannot cluster regions within pre-defined groups. Moreover, k-means will be much faster than hierarchical clustering.*
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
222
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
223 Output
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
224 --------------
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
225
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
226 This is a heatmap based on two bigWig files generated with default settings and k-means clustering.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
227
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
228 .. image:: $PATH_TO_IMAGES/plotHeatmap_example.png
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
229 :width: 600
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
230 :height: 694
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
231
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
232 .. image:: $PATH_TO_IMAGES/plotHeatmap_example02.png
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
233 :width: 600
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
234 :height: 694
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
235
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
236 In addition to the image, ``plotHeatmap`` can also generate the values underlying both the heatmap.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
237
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
238 See the following table for the optional output options:
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
239
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
240 +-----------------------------------+--------------------+-----------------+-----------------+
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
241 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
242 +-----------------------------------+--------------------+-----------------+-----------------+
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
243 | values underlying the heatmap | yes | yes | no |
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
244 +-----------------------------------+--------------------+-----------------+-----------------+
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
245 | values underlying the profile | no | no | yes |
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
246 +-----------------------------------+--------------------+-----------------+-----------------+
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
247 | sorted and/or filtered regions | yes | yes | yes |
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
248 +-----------------------------------+--------------------+-----------------+-----------------+
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
249
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
250 **More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_.
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
251
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
252 -----
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
253
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
254 @REFERENCES@
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
255 ]]>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
256 </help>
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
257 <expand macro="citations" />
6a247ae015cc planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents: 0
diff changeset
258 </tool>