diffbind: diffbind.xml annotate

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

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>

Mercurial > repos > bgruening > diffbind

annotate diffbind.xml @ 17:2605cbdaa7d8 draft