annotate diffbind.xml @ 17:2605cbdaa7d8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
author iuc
date Fri, 15 Dec 2023 19:39:14 +0000
parents 163688bb8f73
children f907216064f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
1 <tool id="diffbind" name="DiffBind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
2 <description> differential binding analysis of ChIP-Seq peak data</description>
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
3 <macros>
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
4 <token name="@TOOL_VERSION@">2.10.0</token>
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
6 <token name="@PROFILE@">22.05</token>
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
7 </macros>
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
8 <xrefs>
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
9 <xref type="bio.tools">diffbind</xref>
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
10 <xref type="bioconductor">diffbind</xref>
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
11 </xrefs>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
12 <requirements>
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-diffbind</requirement>
16
163688bb8f73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
iuc
parents: 15
diff changeset
14 <requirement type="package" version="3.5.1">r-base</requirement>
15
194e3f2c1d86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
iuc
parents: 14
diff changeset
15 <requirement type="package" version="1.20.3">r-getopt</requirement>
194e3f2c1d86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
iuc
parents: 14
diff changeset
16 <requirement type="package" version="0.2.20">r-rjson</requirement>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
17 </requirements>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
18 <stdio>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
19 <regex match="Execution halted"
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
20 source="both"
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
21 level="fatal"
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
22 description="Execution halted." />
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
23 <regex match="Input-Error 01"
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
24 source="both"
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
25 level="fatal"
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
26 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
27 <regex match="Error in"
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
28 source="both"
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
29 level="fatal"
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
30 description="An undefined error occured, please check your input carefully and contact your administrator." />
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
31 </stdio>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
32 <version_command><![CDATA[
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
33 echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
34 ]]></version_command>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
35 <command><![CDATA[
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
36 #import re
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
37 #import json
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
38
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
39 ## Adapted from DESeq2 wrapper
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
40 #set $temp_factor_names = list()
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
41 #set $temp_factor = list()
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
42
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
43 #for $g in $rep_group:
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
44
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
45 #set $peak_files = dict()
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
46 #set $bam_files = dict()
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
47 #set $bam_controls = dict()
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
48
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
49 #for $file in $g.peaks:
14
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
50 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed"
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
51 ln -s '${file}' '${file_name}' &&
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
52 #set $peak_files[str($file.element_identifier)] = str($file_name)
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
53 #end for
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
54
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
55 #for $bam in $g.bamreads:
14
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
56 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier))
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
57 #set $bam_file = $bam_name + "-bamreads.bam"
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
58 #set $bam_index = $bam_name + "-bamreads.bai"
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
59 ln -s '${bam}' '${bam_file}' &&
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
60 ln -s '${bam.metadata.bam_index}' '${bam_index}' &&
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
61 #set $bam_files[str($bam.element_identifier)] = str($bam_file)
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
62 #end for
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
63
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
64 #if len($peak_files.keys()) != len($bam_files.keys())
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
65 >&2 echo "Group $g.groupName: same number of Peak and Bam files needs to be given" && exit 1 &&
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
66 #end if
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
67 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($peak_files.items())]} )
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
68 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_files.items())]} )
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
69
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
70 #if str( $g.bamcontrol ) != 'None':
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
71 #for $ctrl in $g.bamcontrol:
14
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
72 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier))
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
73 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam"
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
74 #set ctrl_index = $ctrl_name + "-bamcontrol.bai"
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
75 #if $ctrl_file not in json.dumps($temp_factor):
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
76 ln -s '${ctrl}' '${ctrl_file}' &&
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
77 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' &&
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
78 #end if
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
79 #set $bam_controls[str($ctrl.element_identifier)] = str($ctrl_file)
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
80 #end for
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
81 #if len($peak_files.keys()) != len($bam_files.keys())
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
82 >&2 echo "Group $g.groupName: same number of Peak and Bam control files needs to be given" && exit 1 &&
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
83 #end if
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
84 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_controls.items())]} )
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
85 #end if
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
86
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
87 #end for
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
88
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
89 $temp_factor.reverse()
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
90 $temp_factor_names.append(["Condition", $temp_factor])
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
91
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
92
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
93 Rscript '$__tool_directory__/diffbind.R'
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
94
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
95 -i '#echo json.dumps(temp_factor_names)#'
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
96 -o '$outfile'
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
97 -t $th
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
98 -f $out.format
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
99 -p '$plots'
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
100
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
101 #if $scorecol:
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
102 -n "$scorecol"
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
103 #end if
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
104 #if $lowerbetter:
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
105 -l "$lowerbetter"
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
106 #end if
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
107 #if $summits:
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
108 -s "$summits"
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
109 #end if
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
110
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
111 #if $out.binding_matrix:
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
112 -b
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
113 #end if
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
114
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
115 #if $out.rdata:
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
116 -r
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
117 #end if
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
118
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
119 #if $out.analysis_info:
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
120 -a
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
121 #end if
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
122
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
123 #if $out.rscript:
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
124 && cp '$__tool_directory__/diffbind.R' '$rscript'
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
125 #end if
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
126 ]]>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
127 </command>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
128 <inputs>
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
129 <repeat name="rep_group" title="Group" min="2" max="2" default="2">
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
130 <param name="groupName" type="text" label="Name"
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
131 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
132 <sanitizer>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
133 <valid initial="string.letters,string.digits"><add value="_" /></valid>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
134 </sanitizer>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
135 <validator type="empty_field" />
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
136 </param>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
137 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
14
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
138 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
139 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
140 </repeat>
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
141
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
142 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)">
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
143 <sanitizer>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
144 <valid initial="string.digits"/>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
145 </sanitizer>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
146 </param>
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
147 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" />
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
148 <param name="summits" type="integer" min="0" optional="True" label="Summits" help="Extend peaks Nbp up- and downstream of the summit. For punctate peaks it is advisable to extend (e.g. 250bp), see the DiffBind User Guide">
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
149 <sanitizer>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
150 <valid initial="string.digits"/>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
151 </sanitizer>
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
152 </param>
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
153 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
154
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
155 <!-- Output Options -->
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
156 <section name="out" expanded="false" title="Output Options">
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
157 <param name="format" type="select" label="Output Format">
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
158 <option value="interval" selected="True">Interval</option>
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
159 <option value="bed">BED</option>
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
160 <option value="tabular">Tabular (tab-separated)</option>
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
161 </param>
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
162 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" />
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
163 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" />
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
164 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
165 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
166 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/>
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
167 </section>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
168 </inputs>
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
169
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
170 <outputs>
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
171 <data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
172 <change_format>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
173 <when input="out.format" value="bed" format="bed" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
174 <when input="out.format" value="tabular" format="tabular" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
175 </change_format>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
176 </data>
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
177 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots">
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
178 <filter>out['pdf']</filter>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
179 </data>
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
180 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix">
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
181 <filter>out['binding_matrix']</filter>
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
182 </data>
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
183 <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file">
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
184 <filter>out['rdata']</filter>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
185 </data>
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
186 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
187 <filter>out['rscript']</filter>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
188 </data>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
189 <data name="analysis_info" format="txt" from_work_dir="DiffBind_analysis_info.txt" label="${tool.name} on ${on_string}: Analysis info">
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
190 <filter>out['analysis_info']</filter>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
191 </data>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
192 </outputs>
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
193
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
194 <tests>
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
195 <!-- Ensure outputs work -->
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
196 <test expect_num_outputs="6">
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
197 <repeat name="rep_group">
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
198 <param name="groupName" value="Resistant"/>
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
199 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
200 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
201 </repeat>
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
202 <repeat name="rep_group">
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
203 <param name="groupName" value="Responsive"/>
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
204 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
205 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
206 </repeat>
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
207 <param name="scorecol" value="5" />
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
208 <param name="format" value="interval"/>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
209 <param name="pdf" value="True" />
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
210 <param name="binding_matrix" value="True" />
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
211 <param name="rdata" value="True" />
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
212 <param name="rscript" value="True"/>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
213 <param name="analysis_info" value="True"/>
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
214 <output name="outfile" ftype="interval" value="out_diffbind.interval" />
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
215 <output name="plots" value="out_plots.pdf" compare="sim_size" />
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
216 <output name="binding_matrix" value="out_binding_matrix.tab" />
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
217 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/>
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
218 <output name="rscript">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
219 <assert_contents>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
220 <has_text text="write.table"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
221 </assert_contents>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
222 </output>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
223 <output name="analysis_info" compare="sim_size" >
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
224 <assert_contents>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
225 <has_text text="SessionInfo"/>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
226 </assert_contents>
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
227 </output>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
228 </test>
14
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
229 <!-- Ensure control BAMs input works -->
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
230 <test expect_num_outputs="1">
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
231 <repeat name="rep_group">
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
232 <param name="groupName" value="Resistant"/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
233 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
234 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
235 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
236 </repeat>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
237 <repeat name="rep_group">
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
238 <param name="groupName" value="Responsive"/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
239 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
240 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
241 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
242 </repeat>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
243 <param name="scorecol" value="5" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
244 <param name="format" value="interval"/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
245 <output name="outfile" ftype="interval" value="out_diffbind_ctrl.interval" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
246 </test>
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
247 <!-- Ensure BED output works -->
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
248 <test expect_num_outputs="1">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
249 <repeat name="rep_group">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
250 <param name="groupName" value="Resistant"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
251 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
252 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
253 </repeat>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
254 <repeat name="rep_group">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
255 <param name="groupName" value="Responsive"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
256 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
257 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
258 </repeat>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
259 <param name="scorecol" value="5" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
260 <param name="format" value="bed"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
261 <output name="outfile" ftype="bed" value="out_diffbind.bed" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
262 </test>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
263 <!-- Ensure tabular output works -->
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
264 <test expect_num_outputs="1">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
265 <repeat name="rep_group">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
266 <param name="groupName" value="Resistant"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
267 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
268 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
269 </repeat>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
270 <repeat name="rep_group">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
271 <param name="groupName" value="Responsive"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
272 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
273 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
274 </repeat>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
275 <param name="scorecol" value="5" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
276 <param name="format" value="tabular"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
277 <output name="outfile" ftype="tabular" file="out_diffbind.tab" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
278 </test>
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
279 </tests>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
280 <help><![CDATA[
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
281
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
282 .. class:: infomark
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
283
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
284 **What it does**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
285
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
286 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
287 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
288 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously,
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
289 representing different ChIP experiments (antibodies, transcription factor and/or histone
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
290 marks, experimental conditions, replicates) as well as managing the results of multiple peak
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
291 callers.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
292
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
293 The primary emphasis of DiffBind is on identifying sites that are differentially bound
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
294 between two sample groups. It includes functions to support the processing of peak sets,
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
295 including overlapping and merging peak sets, counting sequencing reads overlapping intervals
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
296 in peak sets, and identifying statistically significantly differentially bound sites based on
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
297 evidence of binding affinity (measured by differences in read densities). To this end it uses
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
298 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
299 edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
300 set of standardized plots to aid in binding analysis.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
301
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
302 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
303 examples: the first focusing on the core task of obtaining differentially bound sites based on
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
304 affinity data, the second working through the main plotting routines, the third discussing the
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
305 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail,
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
306 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
307 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
308
14
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents: 13
diff changeset
309 **Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).**
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
310
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
311 -----
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
312
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
313 **Inputs**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
314
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
315 DiffBind works primarily with peaksets, which are sets of genomic intervals representing
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
316 candidate protein binding sites. Each interval consists of a chromosome, a start and end
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
317 position, and usually a score of some type indicating confidence in, or strength of, the peak.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
318 Associated with each peakset are metadata relating to the experiment from which the peakset
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
319 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
320 be associated with each peakset (one for the ChIP data, and optionally another representing
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
321 a control sample)
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
322
17
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
323 Inputs for a group will be sorted by identifier before processing. For each group the corresponding
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
324 sets of peak and BAM files need to be provided. Ideally this is accomplished by providing the data in
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
325 collections.
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
326
2605cbdaa7d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents: 16
diff changeset
327
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
328 **Groups**
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
329
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
330 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above.
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
331
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
332 Example:
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
333
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
334 ============= =============
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
335 **Sample** **Group**
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
336 ------------- -------------
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
337 BT4741 Resistant
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
338 BT4742 Resistant
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
339 MCF71 Responsive
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
340 MCF72 Responsive
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
341 ============= =============
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
342
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
343
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
344 **Peak files**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
345
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
346 Result of your Peak calling experiment in bed format, one file for each sample is required. The peak caller, format and score column can be specified in the tool form above. The default settings expect narrowPeak bed format, which has the score in the 8th column (-log10pvalue), and can be output from MACS2.
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
347
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
348 Example:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
349
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
350 ======= ======= ======= =============== ==============
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
351 1 2 3 4 **5 (Score)**
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
352 ======= ======= ======= =============== ==============
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
353 chr18 215562 216063 peak_16037 56.11
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
354 chr18 311530 312105 peak_16038 222.49
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
355 chr18 356656 357315 peak_16039 92.06
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
356 chr18 371110 372092 peak_16040 123.86
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
357 chr18 395116 396464 peak_16041 1545.39
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
358 chr18 399014 400382 peak_16042 1835.19
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
359 chr18 499134 500200 peak_16043 748.32
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
360 chr18 503518 504552 peak_16044 818.30
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
361 chr18 531672 532274 peak_16045 159.30
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
362 chr18 568326 569282 peak_16046 601.11
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
363 ======= ======= ======= =============== ==============
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
364
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
365 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required.
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
366 * Optional: Control BAM file representing a control dataset. If used, has to be specified for all samples. Note that the DiffBind authors say control reads are best utilized prior to running DiffBind, at the peak calling stage (e.g. with MACS2) and in blacklists, see this `Bioconductor post`_.
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
367
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
368 -----
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
369
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
370 **Outputs**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
371
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
372 This tool outputs
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
373
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
374 * a table of differentially bound sites in Interval, BED or Tabular 0-based format
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
375
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
376 Optionally, under **Output Options** you can choose to output
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
377
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
378 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots)
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
379 * a binding affinity matrix
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
380 * the R script used by this tool
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
381 * an RData file of the R objects generated
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
382 * a text file with information on the analysis (number of Intervals, FriP scores, method used)
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
383
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
384 **Differentially Bound Sites**
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
385
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
386 The default output is Interval format, for information on Interval format see here_. Alternatively, you can choose to output BED or Tabular 0-based format as below. For an explanation of the 0-based and 1-based coordinate systems see this `Biostars post`_.
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
387
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
388 Example - **Interval format**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
389
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
390 ====== ====== ====== ======== ===== ====== ===========================================
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
391 Chrom Start End Name Score Strand **Comment**
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
392 ====== ====== ====== ======== ===== ====== ===========================================
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
393 chr18 394599 396513 DiffBind 0 \. 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
394 chr18 111566 112005 DiffBind 0 \. 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
395 chr18 346463 347342 DiffBind 0 \. 879|5|5.77|3.24|2.52|6.51e-06|0.00303
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
396 chr18 399013 400382 DiffBind 0 \. 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
397 chr18 371109 372102 DiffBind 0 \. 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
398 ====== ====== ====== ======== ===== ====== ===========================================
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
399
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
400 Columns contain the following data:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
401
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
402 * **Chrom**: Chromosome name
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
403 * **Start**: Start position of site
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
404 * **End**: End position of site
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
405 * **Score**: 0
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
406 * **Name**: DiffBind
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
407 * **Strand**: Strand
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
408 * **Comment**: The pipe ("|") separated values in this column correspond to:
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
409
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
410 * *width*: Length of site
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
411 * *Conc*: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
412 * *Conc_Group1*: Mean concentration over the first group (e.g. Responsive)
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
413 * *Conc_Group2*: Mean concentration over second group (e.g. Resistant)
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
414 * *Fold*: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group.
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
415 * *p.value*: P-value confidence measure for identifying these sites as differentially bound
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
416 * *FDR*: a multiple testing corrected FDR p-value
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
417
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
418 Example - **BED format**:
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
419
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
420 ===== ====== ====== ======== ===== ======
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
421 Chrom Start End Name Score Strand
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
422 ===== ====== ====== ======== ===== ======
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
423 chr18 394599 396513 DiffBind 0 \.
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
424 chr18 111566 112005 DiffBind 0 \.
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
425 chr18 346463 347342 DiffBind 0 \.
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
426 chr18 399013 400382 DiffBind 0 \.
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
427 chr18 371109 372102 DiffBind 0 \.
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
428 ===== ====== ====== ======== ===== ======
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
429
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
430 Example - **Tabular format**:
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
431
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
432 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
433 Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
434 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
435 chr18 394599 396513 DiffBind 0 \. 7.15 5.55 7.89 -2.35 7.06E-24 9.84E-21
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
436 chr18 111566 112005 DiffBind 0 \. 5.71 6.53 3.63 2.89 1.27E-08 8.88E-06
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
437 chr18 346463 347342 DiffBind 0 \. 5 5.77 3.24 2.52 6.51E-06 0.00303
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
438 chr18 399013 400382 DiffBind 0 \. 7.62 7 8.05 -1.04 1.04E-05 0.00364
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
439 chr18 371109 372102 DiffBind 0 \. 4.63 3.07 5.36 -2.3 8.10E-05 0.0226
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
440 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
441
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
442
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
443 **Binding Affinity Matrix**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
444
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
445 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
446 differential analysis. Note that this output is a tabular 0-based format.
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
447
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
448 Example:
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
449
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
450 ===== ====== ====== ========= ========= ========== ==========
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
451 Chrom Start End MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
452 ===== ====== ====== ========= ========= ========== ==========
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
453 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
454 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
455 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
456 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
457 chr18 346464 347342 75.63583 40.96941 21.00995 16.80796
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
458 chr18 356560 357362 11.55547 14.70696 57.77737 53.57538
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
459 chr18 371110 372102 8.403982 9.454479 81.93882 82.98932
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
460 chr18 394600 396513 56.72687 43.07040 510.5419 438.0575
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
461 chr18 399014 400382 156.5241 117.6557 558.8648 496.8854
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
462 chr18 498906 500200 767.9138 278.3819 196.4430 181.7361
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
463 ===== ====== ====== ========= ========= ========== ==========
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
464
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
465 -----
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
466
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
467 **More Information**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
468
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
469 Generally, processing data with DiffBind involves five phases:
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
470
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
471 #. Reading in peaksets
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
472 #. Occupancy analysis
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
473 #. Counting reads
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
474 #. Differential binding affinity analysis
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
475 #. Plotting and reporting
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
476
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
477
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
478 **Reading in peaksets**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
479
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
480 The first step is to read in a set of peaksets and associated
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
481 metadata. Peaksets are derived either from ChIP-Seq peak callers, such as **MACS2**, or using some other criterion (e.g. genomic windows, or all the promoter regions
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
482 in a genome). A single experiment can have more than
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
483 one associated peakset; e.g. if multiple peak callers are used for comparison purposes
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
484 each sample would have more than one line in the sample sheet. Once the peaksets
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
485 are read in, a merging function finds all overlapping peaks and derives a single set of
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
486 unique genomic intervals covering all the supplied peaks (a consensus peakset for the
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
487 experiment).
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
488
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
489 **Occupancy analysis**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
490
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
491 Peaksets, especially those generated by peak callers, provide
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
492 an insight into the potential occupancy of the protein being ChIPed for at specific
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
493 genomic loci. After the peaksets have been loaded, it can be useful to perform some
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
494 exploratory plotting to determine how these occupancy maps agree with each other,
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
495 e.g. between experimental replicates (re-doing the ChIP under the same conditions),
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
496 between different peak callers on the same experiment, and within groups of samples
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
497 representing a common experimental condition. DiffBind provides functions to enable
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
498 overlaps to be examined, as well as functions to determine how well similar samples
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
499 cluster together. Beyond quality control, the product of an occupancy analysis may be
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
500 a consensus peakset, representing an overall set of candidate binding sites to be used
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
501 in further analysis.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
502
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
503 **Counting reads**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
504
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
505 Once a consensus peakset has been derived, DiffBind can use the
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
506 supplied sequence read files to count how many reads overlap each interval for each
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
507 unique sample. The peaks in the consensus peakset may be re-centered and trimmed
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
508 based on calculating their summits (point of greatest read overlap) in order to provide
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
509 more standardized peak intervals. The final result of counting is a binding affinity matrix
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
510 containing a (normalized) read count for each sample at every potential binding site.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
511 With this matrix, the samples can be re-clustered using affinity, rather than occupancy,
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
512 data. The binding affinity matrix is used for QC plotting as well as for subsequent
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
513 differential analysis.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
514
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
515 **Differential binding affinity analysis**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
516
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
517 The core functionality of DiffBind is the
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
518 differential binding affinity analysis, which enables binding sites to be identified that
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
519 are statistically significantly differentially bound between sample groups. To accomplish
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
520 this, first a contrast (or contrasts) is established, dividing the samples into groups to
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
521 be compared. Next the core analysis routines are executed, by default using DESeq2.
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
522 This will assign a p-value and FDR to each candidate binding site indicating confidence
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
523 that they are differentially bound.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
524
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
525 **Plotting and reporting**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
526
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
527 Once one or more contrasts have been run, DiffBind provides
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
528 a number of functions for reporting and plotting the results. MA plots give an
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
529 overview of the results of the analysis, while correlation heatmaps and PCA plots show
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
530 how the groups cluster based on differentially bound sites. Boxplots show the distribution
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
531 of reads within differentially bound sites corresponding to whether they gain or
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
532 lose affinity between the two sample groups. A reporting mechanism enables differentially
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
533 bound sites to be extracted for further processing, such as annotation, motif, and
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
534 pathway analyses.
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
535
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
536 -----
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
537
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
538 **References**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
539
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
540 DiffBind Authors: Rory Stark, Gordon Brown (2011)
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
541 Wrapper authors: Bjoern Gruening, Pavankumar Videm
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
542
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
543 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
544 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
545 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
546 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/
13
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
547 .. _here: https://galaxyproject.org/learn/datatypes/#interval
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
parents: 12
diff changeset
548 .. _`Biostars post`: https://www.biostars.org/p/84686/
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents: 10
diff changeset
549
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
550 ]]>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
551 </help>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
552 <citations>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
553 <citation type="doi">doi:10.1038/nature10730</citation>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
554 </citations>
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
555 </tool>