diffbind: diffbind.xml annotate

annotate diffbind.xml @ 7:681dedc42aca draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830

author	iuc
date	Sun, 28 Jan 2018 04:26:11 -0500
parents	6031247f61d4
children

rev	line source
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	1 <tool id="diffbind" name="DiffBind" version="2.6.5.0">
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	2 <description> differential binding analysis of ChIP-Seq peak data</description>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	3 <requirements>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	4 <requirement type="package" version="2.6.5">bioconductor-diffbind</requirement>
6 6031247f61d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 3bc676ca60e837f8aca261d0b7860128b3474a5c bgruening parents: 5 diff changeset	5 <requirement type="package" version="1.20.0">r-getopt</requirement>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	6 <!--added rmysql requirement to remove: "Warning: namespace ‘RMySQL’ is not available"-->
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	7 <requirement type="package" version="0.10.11">r-rmysql</requirement>
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	8 </requirements>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	9 <stdio>
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	10 <regex match="Execution halted"
9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	11 source="both"
9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	12 level="fatal"
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	13 description="Execution halted." />
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	14 <regex match="Input-Error 01"
9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	15 source="both"
9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	16 level="fatal"
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	17 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	18 <regex match="Error in"
9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	19 source="both"
9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	20 level="fatal"
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	21 description="An undefined error occured, please check your intput carefully and contact your administrator." />
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	22 </stdio>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	23 <version_command><![CDATA[
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	24 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: ")," getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")", rmysql version" $(R --vanilla --slave -e "library(rmysql); cat(sessionInfo()\$otherPkgs\$rmysql\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	25 ]]></version_command>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	26 <command><![CDATA[
3 d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	27 ## seems that diffbind also needs file extensions to work properly
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	28 #set $counter = 1
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	29 #for $sample in $samples:
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	30 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	31 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	32 #if str( $sample.bamcontrol ) != 'None':
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	33 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	34 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	35 #end if
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	36 #set $counter = $counter + 1
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	37 #end for
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	38
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	39 Rscript '$__tool_directory__/diffbind.R'
3 d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	40 -i $infile
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	41 -o '$outfile'
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	42 -p '$plots'
3 d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	43 -f $format
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	44 -t $th
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	45
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	46 #if $binding_affinity_matrix:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	47 -b
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	48 #end if
3 d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	49 ]]>
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	50 </command>
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	51 <configfiles>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	52 <configfile name="infile"><![CDATA[
3 d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	53 #set $counter = 1
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	54 #for $sample in $samples:
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	55 #if str( $sample.bamcontrol ) != 'None' and $counter == 1:
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	56 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	57 #elif $counter == 1:
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	58 SampleID,Tissue,Factor,Condition,Replicate,bamReads,Peaks
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	59 #end if
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	60 #if str( $sample.bamcontrol ) != 'None':
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	61 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	62 #else:
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	63 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,$sample.peaks
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	64 #end if
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	65 #set $counter = $counter + 1
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	66 #end for]]></configfile>
3 d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	67 </configfiles>
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	68 <inputs>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	69 <repeat name="samples" title="Samples" min="2">
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	70 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	71 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	72 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	73 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	74 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	75 <param name="bamreads" type="data" format="bam" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	76 <param name="bamcontrol" type="data" format="bam" optional="True" label="Control BAM file" help="If specifying a control BAM file for this sample, then all samples are required to specify one."/>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	77 <param name="peaks" type="data" format="bed" label="Peak file" help="Result of your Peak calling experiment."/>
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	78 </repeat>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	79 <param name="th" type="float" value="1" min="0" max="1"
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	80 label="FDR Threshold"
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	81 help="Significance threshold; all sites with FDR less than or equal to this value will be included in the report. A value of 1 will include all binding sites in the report. Default: 1"/>
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	82 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	83 label="Visualising the analysis results"
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	84 help="output an additional PDF file" />
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	85 <param name="format" type="select" label="Output Format">
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	86 <option value="bed">BED</option>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	87 <option value="gff">GFF</option>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	88 <option value="wig">WIG</option>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	89 </param>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	90 <param name="binding_affinity_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" />
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	91 </inputs>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	92 <outputs>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	93 <data name="outfile" format="bed" label="Differential binding sites on ${on_string}">
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	94 <change_format>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	95 <when input="format" value="wig" format="wig" />
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	96 <when input="format" value="gff" format="gff" />
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	97 </change_format>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	98 </data>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	99 <data name="plots" format="pdf" label="Differential binding sites on ${on_string}">
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	100 <filter>pdf == True</filter>
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	101 </data>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	102 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="Differential binding sites on ${on_string}">
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	103 <filter>binding_affinity_matrix == True</filter>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	104 </data>
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	105 </outputs>
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	106 <tests>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	107 <test>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	108 <repeat name="samples">
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	109 <param name="sample_id" value="BT4741" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	110 <param name="tissue" value="BT474" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	111 <param name="factor" value="ER" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	112 <param name="condition" value="Resistant" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	113 <param name="replicate" value="1" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	114 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	115 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	116 </repeat>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	117 <repeat name="samples">
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	118 <param name="sample_id" value="BT4742" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	119 <param name="tissue" value="BT474" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	120 <param name="factor" value="ER" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	121 <param name="condition" value="Resistant" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	122 <param name="replicate" value="2" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	123 <param name="bamreads" ftype="bam" value="BT474_ER_2.bam" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	124 <param name="peaks" ftype="bed" value="BT474_ER_2.bed.gz" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	125 </repeat>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	126 <repeat name="samples">
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	127 <param name="sample_id" value="MCF71" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	128 <param name="tissue" value="MCF7" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	129 <param name="factor" value="ER" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	130 <param name="condition" value="Responsive" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	131 <param name="replicate" value="1" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	132 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	133 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	134 </repeat>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	135 <repeat name="samples">
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	136 <param name="sample_id" value="MCF72" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	137 <param name="tissue" value="MCF7" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	138 <param name="factor" value="ER" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	139 <param name="condition" value="Responsive" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	140 <param name="replicate" value="2" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	141 <param name="bamreads" ftype="bam" value="MCF7_ER_2.bam" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	142 <param name="peaks" ftype="bed" value="MCF7_ER_2.bed.gz" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	143 </repeat>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	144 <param name="pdf" value="True" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	145 <param name="binding_affinity_matrix" value="True" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	146 <output name="outfile" value="out_diffbind.bed" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	147 <output name="binding_matrix" value="out_binding.matrix" />
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	148 </test>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	149 </tests>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	150 <help><![CDATA[
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	151
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	152 .. class:: infomark
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	153
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	154 What it does
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	155
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	156 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	157 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	158 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously,
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	159 representing different ChIP experiments (antibodies, transcription factor and/or histone
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	160 marks, experimental conditions, replicates) as well as managing the results of multiple peak
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	161 callers.
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	162
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	163 The primary emphasis of DiffBind is on identifying sites that are differentially bound
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	164 between two sample groups. It includes functions to support the processing of peak sets,
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	165 including overlapping and merging peak sets, counting sequencing reads overlapping intervals
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	166 in peak sets, and identifying statistically significantly differentially bound sites based on
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	167 evidence of binding affinity (measured by differences in read densities). To this end it uses
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	168 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	169 edgeR and DESeq2 ). Additionally, the package builds on Rgraphics routines to provide a
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	170 set of standardized plots to aid in binding analysis.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	171
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	172 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	173 examples: the first focusing on the core task of obtaining differentially bound sites based on
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	174 affinity data, the second working through the main plotting routines, the third discussing the
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	175 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail,
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	176 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	177 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	178
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	179 Note DiffBind requires a minimum of four samples (two groups with two replicates each).
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	180
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	181 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	182 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	183 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	184
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	185 Inputs
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	186
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	187 DiffBind works primarily with peaksets, which are sets of genomic intervals representing
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	188 candidate protein binding sites. Each interval consists of a chromosome, a start and end
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	189 position, and usually a score of some type indicating confidence in, or strength of, the peak.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	190 Associated with each peakset are metadata relating to the experiment from which the peakset
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	191 was derived. Additionally, files containing mapped sequencing reads (generally .bam files) can
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	192 be associated with each peakset (one for the ChIP data, and optionally another representing
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	193 a control sample)
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	194
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	195 Sample Information
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	196
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	197 You have to specify your sample information in the tool form above.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	198
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	199 Example:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	200
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	201 ============= ========== ========== ============= =============
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	202 SampleID Tissue Factor Condition Replicate
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	203 ------------- ---------- ---------- ------------- -------------
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	204 BT4741 BT474 ER Resistant 1
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	205 BT4742 BT474 ER Resistant 2
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	206 MCF71 MCF7 ER Responsive 1
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	207 MCF72 MCF7 ER Responsive 2
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	208 MCF73 MCF7 ER Responsive 3
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	209 T47D1 T47D ER Responsive 1
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	210 T47D2 T47D ER Responsive 2
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	211 MCF7r1 MCF7 ER Resistant 1
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	212 MCF7r2 MCF7 ER Resistant 2
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	213 ZR751 ZR75 ER Responsive 1
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	214 ZR752 ZR75 ER Responsive 2
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	215 ============= ========== ========== ============= =============
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	216
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	217 Or provide a sample sheet tabular file such as below.
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	218
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	219 Example:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	220
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	221 ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ==========
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	222 SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	223 ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ==========
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	224 BT4741 BT474 ER Resistant Full-Media 1 Chr18_BT474_ER_1.bam BT474c Chr18_BT474_input.bam BT474_ER_1.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	225 BT4742 BT474 ER Resistant Full-Media 2 Chr18_BT474_ER_2.bam BT474c Chr18_BT474_input.bam BT474_ER_2.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	226 MCF71 MCF7 ER Responsive Full-Media 1 Chr18_MCF7_ER_1.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_1.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	227 MCF72 MCF7 ER Responsive Full-Media 2 Chr18_MCF7_ER_2.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_2.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	228 MCF73 MCF7 ER Responsive Full-Media 3 Chr18_MCF7_ER_3.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_3.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	229 T47D1 T47D ER Responsive Full-Media 1 Chr18_T47D_ER_1.bam T47Dc Chr18_T47D_input.bam T47D_ER_1.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	230 T47D2 T47D ER Responsive Full-Media 2 Chr18_T47D_ER_2.bam T47Dc Chr18_T47D_input.bam T47D_ER_2.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	231 MCF7r1 MCF7 ER Resistant Full-Media 1 Chr18_TAMR_ER_1.bam TAMRc Chr18_TAMR_input.bam TAMR_ER_1.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	232 MCF7r2 MCF7 ER Resistant Full-Media 2 Chr18_TAMR_ER_2.bam TAMRc Chr18_TAMR_input.bam TAMR_ER_2.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	233 ZR751 ZR75 ER Responsive Full-Media 1 Chr18_ZR75_ER_1.bam ZR75c Chr18_ZR75_input.bam ZR75_ER_1.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	234 ZR752 ZR75 ER Responsive Full-Media 2 Chr18_ZR75_ER_2.bam ZR75c Chr18_ZR75_input.bam ZR75_ER_2.bed.gz bed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	235 ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ==========
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	236
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	237
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	238 Peak files
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	239
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	240 Result of your Peak calling experiment in bed format, one file for each sample is required.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	241
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	242 Example:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	243
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	244 ======= ======= ======= =============== =======
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	245 1 2 3 4 5
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	246 ======= ======= ======= =============== =======
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	247 chr18 215562 216063 MACS_peak_16037 56.11
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	248 chr18 311530 312105 MACS_peak_16038 222.49
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	249 chr18 356656 357315 MACS_peak_16039 92.06
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	250 chr18 371110 372092 MACS_peak_16040 123.86
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	251 chr18 395116 396464 MACS_peak_16041 1545.39
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	252 chr18 399014 400382 MACS_peak_16042 1835.19
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	253 chr18 499134 500200 MACS_peak_16043 748.32
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	254 chr18 503518 504552 MACS_peak_16044 818.30
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	255 chr18 531672 532274 MACS_peak_16045 159.30
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	256 chr18 568326 569282 MACS_peak_16046 601.11
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	257 ======= ======= ======= =============== =======
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	258
3 d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	259 * BAM file which contains the mapped sequencing reads can be associated with each peakset
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	260 * Control BAM file represents a control dataset and are optional, but have to specified for all when used.
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	261
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	262
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	263 Outputs
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	264
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	265 As output format you can choose BED, GFF, WIG.
9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	266
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	267 Example:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	268
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	269 ======== ====== =======+
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	270 seqnames ranges strand Conc Conc_Resistant
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	271
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	272 2452 chr18 [64490686, 64491186] * \| 6.36 1.39
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	273 1291 chr18 [34597713, 34598213] * \| 5.33 0.22
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	274 976 chr18 [26860997, 26861497] * \| 7.3 3.13
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	275 2338 chr18 [60892900, 60893400] * \| 7.13 1.84
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	276 2077 chr18 [55569087, 55569587] * \| 5.52 1.89
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	277
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	278 Conc_Responsive Fold p-value FDR
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	279 <numeric> <numeric> <numeric> <numeric>
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	280 2452 7 -5.61 3.57e-10 1.02e-06
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	281 1291 5.97 -5.75 1.1e-09 1.57e-06
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	282 976 7.92 -4.79 1.1e-08 1.05e-05
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	283 2338 7.77 -5.93 1.68e-08 1.17e-05
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	284 2077 6.13 -4.23 2.36e-08 1.17e-05
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	285
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	286 The value columns show the
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	287 Conc mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	288 Conc_Resistant mean concentration over the first (Resistant) group
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	289 Conc_Responsive mean concentration over second (Responsive) group
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	290 Fold column shows the difference in mean concentrations between the two groups (Conc_Resistant - Conc_Responsive), with a positive value indicating increased binding affinity in the Resistant group and a negative value indicating increased binding affinity in the Responsive group.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	291 p-value confidence measure for identifying these sites as differentially bound
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	292 FDR a multiple testing corrected FDR p-value
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	293
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	294
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	295 Binding Affinity Matrix
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	296
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	297 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
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	298 differential analysis.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	299
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	300 Example:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	301
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	302 ====== ====== ====== ========== ========== ========= ====== ========= ====
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	303 ID Tissue Factor Condition Treatment Replicate Caller Intervals FRiP
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	304 ====== ====== ====== ========== ========== ========= ====== ========= ====
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	305 BT4741 BT474 ER Resistant Full-Media 1 counts 2845 0.16
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	306 BT4742 BT474 ER Resistant Full-Media 2 counts 2845 0.15
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	307 MCF71 MCF7 ER Responsive Full-Media 1 counts 2845 0.27
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	308 MCF72 MCF7 ER Responsive Full-Media 2 counts 2845 0.17
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	309 MCF73 MCF7 ER Responsive Full-Media 3 counts 2845 0.23
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	310 T47D1 T47D ER Responsive Full-Media 1 counts 2845 0.10
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	311 T47D2 T47D ER Responsive Full-Media 2 counts 2845 0.06
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	312 MCF7r1 MCF7 ER Resistant Full-Media 1 counts 2845 0.20
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	313 MCF7r2 MCF7 ER Resistant Full-Media 2 counts 2845 0.13
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	314 ZR751 ZR75 ER Responsive Full-Media 1 counts 2845 0.32
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	315 ZR752 ZR75 ER Responsive Full-Media 2 counts 2845 0.22
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	316 ====== ====== ====== ========== ========== ========= ====== ========= ====
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	317
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	318
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	319
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	320 More Information
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	321
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	322 Generally, processing data with DiffBind involves five phases:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	323
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	324 #. Reading in peaksets
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	325 #. Occupancy analysis
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	326 #. Counting reads
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	327 #. Differential binding affinity analysis
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	328 #. Plotting and reporting
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	329
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	330
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	331 * Reading in peaksets:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	332
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	333 The first step is to read in a set of peaksets and associated
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	334 metadata. Peaksets are derived either from ChIP-Seq peak callers, such as MACS
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	335 ([1]), or using some other criterion (e.g. genomic windows, or all the promoter regions
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	336 in a genome). The easiest way to read in peaksets is using a comma-separated value
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	337 (csv) sample sheet with one line for each peakset. (Spreadsheets in Excel® format, with
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	338 a .xls or .xlsx suffix, are also accepted.) A single experiment can have more than
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	339 one associated peakset; e.g. if multiple peak callers are used for comparison purposes
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	340 each sample would have more than one line in the sample sheet. Once the peaksets
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	341 are read in, a merging function finds all overlapping peaks and derives a single set of
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	342 unique genomic intervals covering all the supplied peaks (a consensus peakset for the
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	343 experiment).
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	344
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	345 * Occupancy analysis:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	346
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	347 Peaksets, especially those generated by peak callers, provide
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	348 an insight into the potential occupancy of the protein being ChIPed for at specific
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	349 genomic loci. After the peaksets have been loaded, it can be useful to perform some
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	350 exploratory plotting to determine how these occupancy maps agree with each other,
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	351 e.g. between experimental replicates (re-doing the ChIP under the same conditions),
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	352 between different peak callers on the same experiment, and within groups of samples
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	353 representing a common experimental condition. DiffBind provides functions to enable
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	354 overlaps to be examined, as well as functions to determine how well similar samples
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	355 cluster together. Beyond quality control, the product of an occupancy analysis may be
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	356 a consensus peakset, representing an overall set of candidate binding sites to be used
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	357 in further analysis.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	358
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	359 * Counting reads:
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	360
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	361 Once a consensus peakset has been derived, DiffBind can use the
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	362 supplied sequence read files to count how many reads overlap each interval for each
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	363 unique sample. The peaks in the consensus peakset may be re-centered and trimmed
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	364 based on calculating their summits (point of greatest read overlap) in order to provide
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	365 more standardized peak intervals. The final result of counting is a binding affinity matrix
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	366 containing a (normalized) read count for each sample at every potential binding site.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	367 With this matrix, the samples can be re-clustered using affinity, rather than occupancy,
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	368 data. The binding affinity matrix is used for QC plotting as well as for subsequent
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	369 differential analysis.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	370
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	371 * Differential binding affinity analysis:
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	372
7 681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	373 The core functionality of DiffBind is the
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	374 differential binding affinity analysis, which enables binding sites to be identified that
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	375 are statistically significantly differentially bound between sample groups. To accomplish
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	376 this, first a contrast (or contrasts) is established, dividing the samples into groups to
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	377 be compared. Next the core analysis routines are executed, by default using DESeq2 .
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	378 This will assign a p-value and FDR to each candidate binding site indicating confidence
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	379 that they are differentially bound.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	380
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	381 * Plotting and reporting:
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	382
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	383 Once one or more contrasts have been run, DiffBind provides
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	384 a number of functions for reporting and plotting the results. MA plots give an
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	385 overview of the results of the analysis, while correlation heatmaps and PCA plots show
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	386 how the groups cluster based on differentially bound sites. Boxplots show the distribution
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	387 of reads within differentially bound sites corresponding to whether they gain or
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	388 lose affinity between the two sample groups. A reporting mechanism enables differentially
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	389 bound sites to be extracted for further processing, such as annotation, motif, and
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	390 pathway analyses.
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	391
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	392 References
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	393
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 iuc parents: 6 diff changeset	394 DiffBind Authors: Rory Stark, Gordon Brown (2011)
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	395 Wrapper authors: Bjoern Gruening, Pavankumar Videm
7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	396
1 9e9f85c20d99 Uploaded bgruening parents: 0 diff changeset	397 ]]>
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	398 </help>
3 d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	399 <citations>
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	400 <citation type="doi">doi:10.1038/nature10730</citation>
d6dcb3dd5f8f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7 bgruening parents: 2 diff changeset	401 </citations>
0 7faaf4a5e4e1 Uploaded bgruening parents: diff changeset	402 </tool>

Mercurial > repos > bgruening > diffbind

annotate diffbind.xml @ 7:681dedc42aca draft