Mercurial > repos > bgruening > deeptools_plot_heatmap
annotate plotHeatmap.xml @ 31:e4c7985d4585 draft default tip
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412
author | bgruening |
---|---|
date | Wed, 27 Sep 2023 20:33:53 +0000 |
parents | 25d830337d31 |
children |
rev | line source |
---|---|
30
25d830337d31
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
bgruening
parents:
28
diff
changeset
|
1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@"> |
1
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@ |
19
010e58e9d822
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents:
17
diff
changeset
|
11 --matrixFile '$matrixFile' |
010e58e9d822
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents:
17
diff
changeset
|
12 --outFileName '$outFileName' |
1
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 $output.showOutputSettings == "yes" |
19
010e58e9d822
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents:
17
diff
changeset
|
15 --plotFileFormat '$output.outFileFormat' |
1
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 $outFileNameMatrix: |
19
010e58e9d822
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents:
17
diff
changeset
|
18 --outFileNameMatrix '$outFileNameMatrix' |
1
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 $outFileSortedRegions: |
19
010e58e9d822
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents:
17
diff
changeset
|
22 --outFileSortedRegions '$outFileSortedRegions' |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
23 #end if |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
24 |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
25 #if $output.dpi: |
19
010e58e9d822
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents:
17
diff
changeset
|
26 --dpi '$output.dpi' |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
27 #end if |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
28 #else |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
29 --plotFileFormat 'png' |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
30 #end if |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
31 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
32 #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
|
33 #if $advancedOpt.sortRegions: |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
34 --sortRegions '$advancedOpt.sortRegions' |
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 |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
37 #if $advancedOpt.linesAtTickMarks: |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
38 --linesAtTickMarks |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
39 #end if |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
40 |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
41 #if $advancedOpt.sortUsing: |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
42 --sortUsing '$advancedOpt.sortUsing' |
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 #if $advancedOpt.averageTypeSummaryPlot: |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
46 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot' |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
47 #end if |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
48 |
23
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
49 --plotType '$advancedOpt.plotType' |
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
50 |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
51 #if str($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
|
52 --missingDataColor '$advancedOpt.missingDataColor' |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
53 #end if |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
54 |
17
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
55 #set colorMap = [] |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
56 #for $cmap in $advancedOpt.colorMapRepeat: |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
57 #silent $colorMap.append(str($cmap.colorMap)) |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
58 #end for |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
59 #if len($colorMap) > 0: |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
60 --colorMap #echo " ".join($colorMap)# |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
61 #end if |
17
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
62 |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
63 --alpha '$advancedOpt.alpha' |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
64 #if str($advancedOpt.colorList).strip() != "": |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
65 --colorList $advancedOpt.colorList |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
66 #end if |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
67 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
68 #if str($advancedOpt.zMin).strip() != "": |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
69 --zMin $advancedOpt.zMin |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
70 #end if |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
71 #if str($advancedOpt.zMax).strip() != "": |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
72 --zMax $advancedOpt.zMax |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
73 #end if |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
74 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
75 #if str($advancedOpt.yMin).strip() != "": |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
76 --yMin $advancedOpt.yMin |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
77 #end if |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
78 #if str($advancedOpt.yMax).strip() != "": |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
79 --yMax $advancedOpt.yMax |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
80 #end if |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
81 #if str($advancedOpt.sortUsingSamples).strip() != "": |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
82 --sortUsingSamples $advancedOpt.sortUsingSamples |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
83 #end if |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
84 #if str($advancedOpt.clusterUsingSamples).strip() != "": |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
85 --clusterUsingSamples $advancedOpt.clusterUsingSamples |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
86 #end if |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
87 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
88 --xAxisLabel '$advancedOpt.xAxisLabel' |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
89 --yAxisLabel '$advancedOpt.yAxisLabel' |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
90 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
91 --heatmapWidth $advancedOpt.heatmapWidth |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
92 --heatmapHeight $advancedOpt.heatmapHeight |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
93 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
94 --whatToShow '$advancedOpt.whatToShow' |
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 --startLabel '$advancedOpt.startLabel' |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
97 --endLabel '$advancedOpt.endLabel' |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
98 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
99 --refPointLabel '$advancedOpt.referencePointLabel' |
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 #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "": |
22
46992aa30bd6
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e10a444c3d1f7acc6fbf8c8ffd51cedb47a083d0
bgruening
parents:
21
diff
changeset
|
102 --samplesLabel $advancedOpt.samplesLabel |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
103 #end if |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
104 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
105 #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "": |
22
46992aa30bd6
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e10a444c3d1f7acc6fbf8c8ffd51cedb47a083d0
bgruening
parents:
21
diff
changeset
|
106 --regionsLabel $advancedOpt.regionsLabel |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
107 #end if |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
108 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
109 #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
|
110 --plotTitle '$advancedOpt.plotTitle' |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
111 #end if |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
112 |
23
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
113 --legendLocation '$advancedOpt.legendLocation' |
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
114 |
17
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
115 --labelRotation '$advancedOpt.labelRotation' |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
116 |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
117 $advancedOpt.perGroup |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
118 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
119 @KMEANS_CLUSTERING@ |
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 #end if |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
122 ]]> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
123 </command> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
124 <inputs> |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
125 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
126 label="Matrix file from the computeMatrix tool" help=""/> |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
127 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
128 <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
|
129 <expand macro="input_image_file_format" /> |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
130 <expand macro="output_dpi" /> |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
131 <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
|
132 </expand> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
133 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
134 <conditional name="advancedOpt" > |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
135 <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
|
136 <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
|
137 <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
|
138 </param> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
139 <when value="no" /> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
140 <when value="yes"> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
141 <expand macro="sortRegions" /> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
142 <expand macro="sortUsing" /> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
143 <param argument="--sortUsingSamples" type="text" |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
144 label="List of samples to be used for sorting" |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
145 help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting. |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
146 If no value is set, it uses all samples. Example: 1 3 (space separated!)" /> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
147 <sanitizer> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
148 <valid initial="string.printable"> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
149 <add value=" "/> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
150 </valid> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
151 </sanitizer> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
152 <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue="" |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
153 label="Draw dashed lines in heatmap above all tick marks?" /> |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
154 <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
|
155 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
|
156 help=""> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
157 <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
|
158 <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
|
159 <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
|
160 <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
|
161 <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
|
162 <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
|
163 </param> |
23
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
164 <param argument="--plotType" type="select" label="Type of summary plot"> |
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
165 <option value="lines">plot the profile line based on the statistic selected above.</option> |
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
166 <option value="fill">fills the region between zero and the profile.</option> |
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
167 <option value="se">color the region between the profile and the standard error.</option> |
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
168 <option value="std">color the region between the profile and the standard deviation.</option> |
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
169 </param> |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
170 <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
|
171 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
|
172 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
|
173 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
|
174 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
|
175 |
17
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
176 <repeat name="colorMapRepeat" title="Colormap to use for each sample" |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
177 help="A different colormap can be applied to each column of the heatmap. If you select fewer colormaps than you have samples in your matrix, then the select colormap(s) will be repeated (e.g., if you select one colormap then it will be applied to all samples)."> |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
178 <expand macro="colorMap" /> |
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
179 </repeat> |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
180 <param argument="--alpha" type="float" value="1.0" min="0.0" |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
181 max="1.0" optional="True" |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
182 label="Alpha channel (transparency)" |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
183 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
184 be between 0 and 1. A value of 0.0 would be fully transparent." /> |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
185 |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
186 <param argument="--colorList" type="text" value="" optional="True" |
8
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
187 label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas" |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
188 help="The color of the heatmaps can be specified as a list of colors separated by comas with |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
189 not space in between. For example: white,blue white,green will set a color map from white |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
190 to blue for the first heatmap and for white to green for the next heatmap."/> |
ca218dae7902
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
1
diff
changeset
|
191 <expand macro="zMin_zMax" /> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
192 <param argument="--yMin" type="float" value="" optional="True" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
193 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
194 <param argument="--yMax" type="float" value="" optional="True" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
195 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
196 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
197 label="The x-axis label" help="" /> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
198 <param argument="--yAxisLabel" type="text" value="genes" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
199 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
|
200 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
201 <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
|
202 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
|
203 <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
|
204 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
|
205 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
206 <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
|
207 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
|
208 <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
|
209 <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
|
210 <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
|
211 </param> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
212 |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
213 <param argument="--startLabel" type="text" value="TSS" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
214 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
|
215 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. "peak start"." /> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
216 <param argument="--endLabel" type="text" value="TES" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
217 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
|
218 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
|
219 |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
220 <param argument="--referencePointLabel" type="text" value="TSS" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
221 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
|
222 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. "peak start" etc." /> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
223 <param argument="--samplesLabel" type="text" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
224 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
|
225 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
|
226 spaces and quoted if a label itself contains a space E.g. label-1 "label 2""> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
227 <sanitizer> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
228 <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
|
229 </valid> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
230 </sanitizer> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
231 </param> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
232 <param argument="--regionsLabel" type="text" |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
233 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
|
234 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
|
235 If a label itself contains a space, then quotes are needed. |
11
c1ff5c446073
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
bgruening
parents:
8
diff
changeset
|
236 For example, label_1 "label 2"" /> |
1
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 <expand macro="plotTitle" /> |
23
751adcc1ce82
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents:
22
diff
changeset
|
239 <expand macro="legendLocation" /> |
17
0d6dfbd66443
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
11
diff
changeset
|
240 <expand macro="labelRotation" /> |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
241 <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
|
242 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
|
243 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
|
244 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
245 <expand macro="kmeans_clustering" /> |
28
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
246 <param argument="--clusterUsingSamples" type="text" |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
247 label="List of samples to be used for clustering" |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
248 help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering. |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
249 If no value is set, it uses all samples. Example: 1 3 (space separated!)"/> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
250 <sanitizer> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
251 <valid initial="string.printable"> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
252 <add value=" "/> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
253 </valid> |
42cb23d80271
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
bgruening
parents:
23
diff
changeset
|
254 </sanitizer> |
1
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
255 </when> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
256 </conditional> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
257 </inputs> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
258 <outputs> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
259 <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
|
260 <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
|
261 <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
|
262 </outputs> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
263 <tests> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
264 <test> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
265 <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
|
266 <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
|
267 </test> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
268 <test> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
269 <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
|
270 <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
|
271 <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
|
272 <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
|
273 </test> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
274 </tests> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
275 <help> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
276 <![CDATA[ |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
277 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
278 What it does |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
279 -------------- |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
280 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
281 ``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
|
282 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
|
283 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
284 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
|
285 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
|
286 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
287 **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
|
288 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
289 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
|
290 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
291 **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
|
292 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
293 Output |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
294 -------------- |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
295 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
296 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
|
297 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
298 .. 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
|
299 :width: 600 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
300 :height: 694 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
301 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
302 .. 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
|
303 :width: 600 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
304 :height: 694 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
305 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
306 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
|
307 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
308 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
|
309 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
310 +-----------------------------------+--------------------+-----------------+-----------------+ |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
311 | **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
|
312 +-----------------------------------+--------------------+-----------------+-----------------+ |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
313 | 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
|
314 +-----------------------------------+--------------------+-----------------+-----------------+ |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
315 | 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
|
316 +-----------------------------------+--------------------+-----------------+-----------------+ |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
317 | 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
|
318 +-----------------------------------+--------------------+-----------------+-----------------+ |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
319 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
320 **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
|
321 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
322 ----- |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
323 |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
324 @REFERENCES@ |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
325 ]]> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
326 </help> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
327 <expand macro="citations" /> |
6a247ae015cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
bgruening
parents:
0
diff
changeset
|
328 </tool> |