annotate plotEnrichment.xml @ 21:c03c3384cd81 draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 14:47:18 +0000
parents e65d16fb2724
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
21
c03c3384cd81 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
bgruening
parents: 18
diff changeset
1 <tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
2 <description>plots read/fragment coverage over sets of regions</description>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
3 <macros>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
4 <token name="@BINARY@">plotEnrichment</token>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
5 <import>deepTools_macros.xml</import>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
6 </macros>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
8 <command>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
9 <![CDATA[
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
10 @multiple_input_bams@
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
11 @BINARY@
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
12 @THREADS@
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
13
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
14 --plotFile '$outFileName'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
15
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
16 --bamfiles #echo " ".join($files)#
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
17 --labels #echo " ".join($labels)#
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
18
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
19 @multiple_bed@
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
20
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
21 #if $outRawCounts:
11
36de8f366d51 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents: 9
diff changeset
22 --outRawCounts '$outFileRawCounts'
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
23 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
24
11
36de8f366d51 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents: 9
diff changeset
25 --plotFileFormat '$outFileFormat'
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
26
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
27 #if str($region).strip() != "":
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
28 --region '$region'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
29 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
30
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
31 #if $advancedOpt.showAdvancedOpt == "yes"
17
d9114ef1c8a5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
bgruening
parents: 14
diff changeset
32 #if $advancedOpt.attributeKey:
d9114ef1c8a5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
bgruening
parents: 14
diff changeset
33 --attributeKey '$advancedOpt.attributeKey'
d9114ef1c8a5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
bgruening
parents: 14
diff changeset
34 #end if
d9114ef1c8a5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
bgruening
parents: 14
diff changeset
35
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
36 #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
37 --labels $advancedOpt.labels
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
38 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
39
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
40 #if $advancedOpt.regionLabels and str($advancedOpt.regionLabels).strip() != "":
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
41 --regionLabels $advancedOpt.regionLabels
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
42 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
43
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
44 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
45 --plotTitle '$advancedOpt.plotTitle'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
46 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
47
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
48 $advancedOpt.perSample
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
49
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
50 $advancedOpt.variableScales
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
51
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
52 $advancedOpt.perSample
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
53
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
54 $advancedOpt.variableScales
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
55
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
56 --plotWidth '$advancedOpt.plotWidth'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
57
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
58 --plotHeight '$advancedOpt.plotHeight'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
59
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
60 #if str($advancedOpt.colors).strip() != "":
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
61 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
62 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
63
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
64 --numPlotsPerRow '$advancedOpt.numPlotsPerRow'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
65
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
66 --alpha '$advancedOpt.alpha'
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
67
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
68 @ADVANCED_OPTS_READ_PROCESSING@
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
69
4
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
70 #if $advancedOpt.Offset:
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
71 --Offset $advancedOpt.Offset
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
72 #end if
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
73
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
74 @blacklist@
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
75
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
76 $advancedOpt.keepExons
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
77
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
78 #end if
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
79 ]]>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
80 </command>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
81
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
82 <inputs>
6
a09adc02b84a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 4
diff changeset
83 <expand macro="multiple_input_bams" MIN="1"/>
14
ef1a67ae6e13 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents: 13
diff changeset
84 <expand macro="custom_sample_labels" />
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
85 <expand macro="multiple_bed" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
86
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
87 <expand macro="region_limit_operation" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
88 <expand macro="input_image_file_format" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
89
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
90 <expand macro="advancedOpt_scaffold">
18
e65d16fb2724 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 17
diff changeset
91 <param argument="--attributeKey" type="text" optional="true" size="20" label="Optional attribute key"
17
d9114ef1c8a5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
bgruening
parents: 14
diff changeset
92 help="Instead of deriving the feature label from the feature column, use the value of the given
d9114ef1c8a5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
bgruening
parents: 14
diff changeset
93 attribute key. For example, the gene_biotype. Note that 'None' is used for BED files
d9114ef1c8a5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
bgruening
parents: 14
diff changeset
94 or entries where the attributeKey is not found." />
d9114ef1c8a5 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83
bgruening
parents: 14
diff changeset
95
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
96 <param argument="--plotHeight" type="integer" value="20" min="3"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
97 label="Plot height"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
98 help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
99
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
100 <param argument="--plotWidth" type="integer" value="20" min="1"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
101 label="Plot width"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
102 help="Width in cm. The default value is 20 centimeters. The minimum value is 1 cm." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
103
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
104 <param argument="--labels" type="text" size="30"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
105 label="Labels for the samples (each BAM file) plotted"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
106 help="The default is to use the file name of the sample. The sample labels should be separated by
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
107 spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
108 <sanitizer>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
109 <valid initial="string.printable" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
110 </sanitizer>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
111 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
112
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
113 <param argument="--regionLabels" type="text" size="30"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
114 label="Labels for the features"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
115 help="For BED files, this sets the label for all entries in each file.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
116 For GTF files this is ignored." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
117
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
118 <expand macro="plotTitle" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
119
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
120 <param argument="--alpha" type="float" value="0.9" min="0.0" max="1.0"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
121 label="Alpha channel"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
122 help="The alpha channel value (between 0 and 1). A value of 0 is transparent. Default: 0.9" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
123
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
124 <param argument="--colors" type="text" value="" size="40"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
125 label="List of colors to use for the plotted bars"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
126 help="Color names and html hex strings (e.g. #eeff22) are accepted.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
127 The color names should be separated by spaces. (--colors red blue green)">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
128 <validator type="expression"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
129 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
130 </param>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
131
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
132 <param argument="--perSample" type="boolean" truevalue="--perSample" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
133 label="Create one plot per-sample"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
134 help="Plot per-sample, rather than per-feature." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
135
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
136 <param argument="--variableScales" type="boolean" truevalue="--variableScales" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
137 label="Allow variable scales"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
138 help="By default, the y-axis always goes from 0 to 100. If this option is selected, then the maximum value will vary with the dataset." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
139
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
140 <param argument="--numPlotsPerRow" type="integer" value="4" min="1"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
141 label="Number of plots/row"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
142 help="" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
143
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
144 <expand macro="read_processing_options" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
145
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
146 <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
147 label="Include BED12 exons"
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
148 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
149
4
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
150 <param argument="--Offset" type="text" value="" optional="True"
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
151 label="Offset inside each alignment to use for the signal location."
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
152 help="Uses this offset inside of each read as the signal. This is useful in
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
153 cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
154 should be used to denote where the signal is (rather than the span of the
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
155 whole alignment). This can be paired with the --filterRNAstrand option. Note
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
156 that negative values indicate offsets from the end of each read. A value of
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
157 1 indicates the first base of the alignment (taking alignment orientation
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
158 into account). Likewise, a value of -1 is the last base of the alignment. An
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
159 offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
160 used to specify a range of positions. Note that specifying something like
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
161 --Offset 5 -1 will result in the 5th through last position being used, which
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
162 is equivalent to trimming 4 bases from the 5-prime end of alignments." />
8980933fd546 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 0
diff changeset
163
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
164 <expand macro="blacklist" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
165
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
166 </expand>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
167
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
168 <param argument="--outRawCounts" type="boolean" label="Save percentages to a file" help=""/>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
169
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
170 </inputs>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
171 <outputs>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
172 <expand macro="output_image_file_format_not_nested" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
173 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: percentages">
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
174 <filter>outRawCounts is True</filter>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
175 </data>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
176 </outputs>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
177 <tests>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
178 <test>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
179 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
180 <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
181 <param name="outRawCounts" value="true" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
182 <param name="showAdvancedOpt" value="yes" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
183 <param name="minMappingQuality" value="0" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
184 <param name="regionLabels" value="up down" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
185 <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="1000" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
186 <output name="outFileRawCounts" file="plotEnrichment_output.txt" ftype="tabular" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
187 </test>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
188 </tests>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
189
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
190 <help>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
191 <![CDATA[
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
192
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
193 What it does
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
194 -------------
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
195
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
196 This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed.
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
197
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
198 Output
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
199 --------
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
200
9
084c9358ce76 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 6
diff changeset
201 The output file is a plot in the format specified. A table of the percentages and raw counts can also be created.
0
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
202
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
203 .. image:: $PATH_TO_IMAGES/plotEnrichment_output.png
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
204 :width: 600
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
205 :height: 600
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
206
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
207 -----
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
208
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
209 @REFERENCES@
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
210 ]]>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
211 </help>
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
212 <expand macro="citations" />
4b88c90b6f6e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
bgruening
parents:
diff changeset
213 </tool>