edger_with_design_matrix: edgeR_Differential_Gene

annotate edgeR_Differential_Gene_Expression.xml @ 120:5c94a732bd62 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795

author	yhoogstrate
date	Sat, 12 Dec 2015 05:21:15 -0500
parents	0a05f6a91d71
children	6c90a67a13fa

rev	line source
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	1 <?xml version="1.0" encoding="UTF-8"?>
115 f06dceb5b966 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty yhoogstrate parents: 114 diff changeset	2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.b">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	4
108 a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	5 <macros>
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	6 <import>edgeR_macros.xml</import>
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	7 </macros>
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	8
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	9 <requirements>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	10 <requirement type="package" version="3.11.0">edger</requirement>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	11 </requirements>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	12
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	13 <stdio>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	14 <regex match="Error in[^a-z]+contrasts"
108 a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	15 source="both"
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	16 level="fatal"
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	17 description="Have the design- and expression-matrix been swapped?" />
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	18 <regex match="Error in eval$expr, envir, enclos$"
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	19 source="both"
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	20 level="fatal"
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	21 description="You have most likely used a condition in the contrast, that is not present in the Design matrix" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	22 <regex match="Execution halted"
108 a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	23 source="both"
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	24 level="fatal" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	25 <regex match="Calculating library sizes from column"
108 a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	26 source="stderr"
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	27 level="log" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	28 <regex match="During startup - Warning messages"
108 a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	29 source="stderr"
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	30 level="log" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	31 <regex match="Setting LC_[^ ]+ failed"
108 a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	32 source="stderr"
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	33 level="warning"
a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	34 description="LOCALE has not been set correctly" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	35 </stdio>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	36
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	37 <version_command>echo $(R --version \| grep version \| grep -v GNU)", EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")</version_command>
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	38
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	39 <command><![CDATA[
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	40 #if $analysis_type.analysis_select == "multi_factor"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	41 #set $expression_matrix = $analysis_type.expression_matrix
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	42 #set $design_matrix = $analysis_type.design_matrix
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	43 #set $contrast = $analysis_type.contrast
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	44 #else
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	45 ## Design and Expression matrices do not exist - create them
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	46 #set $expression_matrix = "expression_matrix.txt"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	47 #set $design_matrix = "design_matrix.txt"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	48 #set $contrast = str($analysis_type.factorLevel_condition)+"-"+str($analysis_type.factorLevel_control)
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	49
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	50 ## -- Create expression matrix
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	51 cut -f 1 "$analysis_type.countsFile_control[1]" > gene_ids.column.txt &&
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	52 #for $file in $analysis_type.countsFile_control:
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	53 cut -f 2 "${file}" > "${file}.expression_column.txt" &&
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	54 #end for
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	55 #for $file in $analysis_type.countsFile_condition:
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	56 cut -f 2 "${file}" > "${file}.expression_column.txt" &&
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	57 #end for
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	58
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	59 paste
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	60 gene_ids.column.txt
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	61 #for $file in $analysis_type.countsFile_control:
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	62 "${file}.expression_column.txt"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	63 #end for
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	64 #for $file in $analysis_type.countsFile_condition:
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	65 "${file}.expression_column.txt"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	66 #end for
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	67 > "${expression_matrix}" &&
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	68
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	69 ## -- Create design matrix matrix
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	70 echo "sample-name Condition" >> ${design_matrix} &&
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	71 #for $file in $analysis_type.countsFile_control:
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	72 echo "${file.name} ${analysis_type.factorLevel_control}" >> ${design_matrix} &&
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	73 #end for
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	74 #for $file in $analysis_type.countsFile_condition:
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	75 echo "${file.name} ${analysis_type.factorLevel_condition}" >> ${design_matrix} &&
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	76 #end for
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	77 #end if
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	78
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	79 R --vanilla --slave -f $R_script '--args
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	80 $expression_matrix
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	81 $design_matrix
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	82 $contrast
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	83
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	84 $analysis_report_genes
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	85 $fdr
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	86
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	87 $output_count_edgeR
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	88 $output_cpm
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	89
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	90 /dev/null ### Calculation of FPKM/RPKM should come here
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	91
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	92 #if $output_raw_counts:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	93 $output_raw_counts
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	94 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	95 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	96 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	97
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	98 #if $output_MDSplot_logFC:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	99 $output_MDSplot_logFC
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	100 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	101 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	102 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	103
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	104 #if $output_MDSplot_logFC_coordinates:
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	105 $output_MDSplot_logFC_coordinates
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	106 #else:
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	107 /dev/null
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	108 #end if
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	109
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	110 #if $output_MDSplot_bcv:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	111 $output_MDSplot_bcv
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	112 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	113 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	114 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	115
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	116 #if $output_MDSplot_bcv_coordinates:
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	117 $output_MDSplot_bcv_coordinates
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	118 #else:
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	119 /dev/null
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	120 #end if
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	121
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	122 #if $output_BCVplot:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	123 $output_BCVplot
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	124 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	125 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	126 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	127
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	128 #if $output_MAplot:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	129 $output_MAplot
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	130 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	131 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	132 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	133
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	134 #if $output_PValue_distribution_plot:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	135 $output_PValue_distribution_plot
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	136 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	137 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	138 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	139
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	140 #if $output_hierarchical_clustering_plot:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	141 $output_hierarchical_clustering_plot
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	142 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	143 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	144 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	145
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	146 #if $output_heatmap_plot:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	147 $output_heatmap_plot
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	148 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	149 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	150 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	151
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	152 #if $output_RData_obj:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	153 $output_RData_obj
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	154 #else:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	155 /dev/null
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	156 #end if
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	157
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	158 $output_format_images
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	159 '
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	160 ]]>
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	161 </command>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	162
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	163 <configfiles>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	164 <configfile name="R_script">
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	165 <![CDATA[
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	166
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	167 library(limma,quietly=TRUE) ## quietly to avoid unnecessaity stderr messages
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	168 library(edgeR,quietly=TRUE) ## quietly to avoid unnecessaity stderr messages
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	169 library(splines,quietly=TRUE)## quietly to avoid unnecessaity stderr messages
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	170
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	171 ## Fetch commandline arguments
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	172 args <- commandArgs(trailingOnly = TRUE)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	173
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	174 expression_matrix_file <- args[1]
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	175 design_matrix_file <- args[2]
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	176 contrast <- args[3]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	177
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	178 truncate_table_by_fdr <- args[4]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	179 fdr <- as.double(args[5])
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	180
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	181 output_count_edgeR <- args[6]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	182 output_cpm <- args[7]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	183
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	184 output_xpkm <- args[8] ##FPKM file - to be implemented
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	185
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	186 output_raw_counts <- args[9]
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	187
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	188 output_MDSplot_logFC <- args[10]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	189 output_MDSplot_logFC_coordinates <- args[11]
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	190
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	191 output_MDSplot_bcv <- args[12]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	192 output_MDSplot_bcv_coordinates <- args[13]
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	193
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	194 output_BCVplot <- args[14]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	195 output_MAplot <- args[15]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	196 output_PValue_distribution_plot <- args[16]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	197 output_hierarchical_clustering_plot <- args[17]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	198 output_heatmap_plot <- args[18]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	199 output_RData_obj <- args[19]
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	200 output_format_images <- args[20]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	201
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	202
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	203 ## Obtain read-counts
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	204 expression_matrix <- read.delim(expression_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	205 design_matrix <- read.delim(design_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	206
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	207 colnames(design_matrix) <- make.names(colnames(design_matrix))
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	208
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	209 for(i in 1:ncol(design_matrix)) {
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	210 old <- design_matrix[,i]
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	211 design_matrix[,i] <- make.names(design_matrix[,i])
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	212 if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	213 print("Renaming of factors:")
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	214 print(old)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	215 print("To:")
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	216 print(design_matrix[,i])
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	217 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	218 ## The following line seems to malfunction the script:
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	219 ##design_matrix[,i] <- as.factor(design_matrix[,i])
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	220 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	221
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	222 ## 1) In the expression matrix, you only want to have the samples described in the design matrix
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	223 columns <- match(rownames(design_matrix),colnames(expression_matrix))
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	224 columns <- columns[!is.na(columns)]
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	225 read_counts <- expression_matrix[,columns]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	226
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	227 ## 2) In the design matrix, you only want to have samples of which you really have the counts
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	228 columns <- match(colnames(read_counts),rownames(design_matrix))
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	229 columns <- columns[!is.na(columns)]
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	230 design_matrix <- design_matrix[columns,,drop=FALSE]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	231
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	232 ## Filter for HTSeq predifined counts:
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	233 exclude_HTSeq <- c("no_feature","ambiguous","too_low_aQual","not_aligned","alignment_not_unique")
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	234 exclude_DEXSeq <- c("_ambiguous","_empty","_lowaqual","_notaligned")
118 7e98e8bcfbf7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit e42aebc7a9b64744919668cb9a856b5df8a61387 yhoogstrate parents: 117 diff changeset	235 exclude_STAR <- c("N_unmapped", "N_multimapping", "N_noFeature", "N_ambiguous")
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	236
118 7e98e8bcfbf7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit e42aebc7a9b64744919668cb9a856b5df8a61387 yhoogstrate parents: 117 diff changeset	237 exclude <- match(c(exclude_HTSeq, exclude_DEXSeq, exclude_STAR),rownames(read_counts))
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	238 exclude <- exclude[is.na(exclude)==0]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	239 if(length(exclude) != 0) {
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	240 read_counts <- read_counts[-exclude,]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	241 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	242
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	243
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	244 ## sorting expression matrix with the order of the read_counts
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	245 ##order <- match(colnames(read_counts) , rownames(design_matrix))
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	246 ##read_counts_ordered <- read_counts[,order2]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	247
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	248 empty_samples <- apply(read_counts,2,function(x) sum(x) == 0)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	249 if(sum(empty_samples) > 0) {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	250 write(paste("There are ",sum(empty_samples)," empty samples found:",sep=""),stderr())
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	251 write(colnames(read_counts)[empty_samples],stderr())
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	252 } else {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	253
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	254 dge <- DGEList(counts=read_counts,genes=rownames(read_counts))
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	255
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	256 formula <- paste(c("~0",make.names(colnames(design_matrix))),collapse = " + ")
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	257 design_matrix_tmp <- design_matrix
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	258 colnames(design_matrix_tmp) <- make.names(colnames(design_matrix_tmp))
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	259 design <- model.matrix(as.formula(formula),design_matrix_tmp)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	260 rm(design_matrix_tmp)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	261
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	262 # Filter prefixes
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	263 prefixes = colnames(design_matrix)[attr(design,"assign")]
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	264 avoid = nchar(prefixes) == nchar(colnames(design))
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	265 replacements = substr(colnames(design),nchar(prefixes)+1,nchar(colnames(design)))
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	266 replacements[avoid] = colnames(design)[avoid]
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	267 colnames(design) = replacements
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	268
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	269 # Do normalization
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	270 write("Calculating normalization factors...",stdout())
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	271 dge <- calcNormFactors(dge)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	272 write("Estimating common dispersion...",stdout())
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	273 dge <- estimateGLMCommonDisp(dge,design)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	274 write("Estimating trended dispersion...",stdout())
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	275 dge <- estimateGLMTrendedDisp(dge,design)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	276 write("Estimating tagwise dispersion...",stdout())
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	277 dge <- estimateGLMTagwiseDisp(dge,design)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	278
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	279
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	280 # hierarchical clustering makes use of the distance of the MDS
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	281 if(output_MDSplot_logFC != "/dev/null" \|\| output_MDSplot_logFC_coordinates != "/dev/null" \|\| output_hierarchical_clustering_plot != "/dev/null") {
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	282 write("Calculating MDS plot (logFC method)",stdout())
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	283 n_dim <- nrow(dge\$samples)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	284 mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	285 dev.off()# Kill it
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	286
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	287 # Reset to primary dimensions
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	288 mds_distance_logFC\$x = mds_distance_logFC\$cmdscale.out[,1]
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	289 mds_distance_logFC\$y = mds_distance_logFC\$cmdscale.out[,2]
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	290
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	291 if(output_MDSplot_logFC != "/dev/null") {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	292 write("Creating MDS plot (logFC method)",stdout())
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	293 if(output_format_images == "pdf") {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	294 pdf(output_MDSplot_logFC,height=14,width=14)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	295 } else if(output_format_images == "svg") {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	296 svg(output_MDSplot_logFC,height=14,width=14)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	297 } else {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	298 ## png(output_MDSplot_logFC)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	299 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	300
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	301 bitmap(output_MDSplot_logFC,type="png16m",height=73,width=73)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	302 }
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	303
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	304 diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x))
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	305 diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y))
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	306 plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2")
115 f06dceb5b966 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty yhoogstrate parents: 114 diff changeset	307 points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	308 text(mds_distance_logFC\$x,mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	309 rm(diff_x,diff_y)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	310
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	311 dev.off()
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	312 }
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	313
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	314 if(output_MDSplot_logFC_coordinates != "/dev/null") {
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	315 n_dim <- ncol(mds_distance_logFC\$cmdscale.out)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	316 colnames(mds_distance_logFC\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_")
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	317 export <- data.frame(samples=rownames(mds_distance_logFC\$cmdscale.out),mds_distance_logFC\$cmdscale.out)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	318 row.names(export) <- NULL
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	319 write.table(file=output_MDSplot_logFC_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	320 }
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	321 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	322
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	323
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	324 if(output_MDSplot_bcv != "/dev/null" \|\| output_MDSplot_bcv_coordinates != "/dev/null" ) {
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	325 write("Creating MDS plot (bcv method)",stdout())
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	326
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	327 ## 1. First create a virtual plot to obtain the desired coordinates
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	328 n_dim <- nrow(dge\$samples)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	329 mds_distance_BCV <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	330 dev.off()
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	331
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	332 if(output_MDSplot_logFC != "/dev/null") {
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	333 ## 2. Re-plot the coordinates in a new figure with the size and settings.
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	334 if(output_format_images == "pdf") {
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	335 pdf(output_MDSplot_bcv,height=14,width=14)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	336 } else if(output_format_images == "svg") {
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	337 svg(output_MDSplot_bcv,height=14,width=14)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	338 } else {
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	339 ## png(output_MDSplot_bcv)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	340 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	341
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	342 bitmap(output_MDSplot_bcv,type="png16m",height=73,width=73)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	343 }
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	344
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	345 diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	346 diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	347 plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	348 points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	349 text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	350 rm(diff_x,diff_y)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	351
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	352 dev.off()
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	353 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	354
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	355 if(output_MDSplot_bcv_coordinates != "/dev/null") {
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	356 n_dim <- ncol(mds_distance_BCV\$cmdscale.out)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	357 colnames(mds_distance_BCV\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_")
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	358 export <- data.frame(samples=rownames(mds_distance_BCV\$cmdscale.out),mds_distance_BCV\$cmdscale.out)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	359 row.names(export) <- NULL
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	360 write.table(file=output_MDSplot_bcv_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE)
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	361 }
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	362 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	363
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	364
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	365 if(output_BCVplot != "/dev/null") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	366 write("Creating Biological coefficient of variation plot",stdout())
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	367
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	368 if(output_format_images == "pdf") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	369 pdf(output_BCVplot)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	370 } else if(output_format_images == "svg") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	371 svg(output_BCVplot)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	372 } else {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	373 ## png(output_BCVplot)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	374 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	375
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	376 bitmap(output_BCVplot,type="png16m",width=10.53,height=73)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	377 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	378
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	379 plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	380 dev.off()
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	381 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	382
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	383
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	384 write("Fitting GLM...",stdout())
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	385 fit <- glmFit(dge,design)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	386
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	387 write(paste("Performing likelihood ratio test: ",contrast,sep=""),stdout())
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	388 cont <- c(contrast)
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	389 cont <- makeContrasts(contrasts=cont, levels=design)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	390
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	391 lrt <- glmLRT(fit, contrast=cont[,1])
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	392 write(paste("Exporting DGE results to file...",output_count_edgeR,sep=""),stdout())
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	393
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	394 if(truncate_table_by_fdr =="all") {
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	395 write.table(file=output_count_edgeR,topTags(lrt,n=nrow(read_counts))\$table,sep="\t",row.names=TRUE,col.names=NA)
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	396 }
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	397 else {
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	398 write.table(file=output_count_edgeR,subset(topTags(lrt,n=nrow(read_counts))\$table, FDR < fdr),sep="\t",row.names=TRUE,col.names=NA)
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	399 }
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	400 write.table(file=output_cpm,cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	401
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	402 ## todo EXPORT FPKM
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	403 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	404
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	405 if(output_MAplot != "/dev/null" \|\| output_PValue_distribution_plot != "/dev/null") {
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	406 etable <- topTags(lrt, n=nrow(dge))\$table
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	407 etable <- etable[order(etable\$FDR), ]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	408
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	409 if(output_MAplot != "/dev/null") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	410 write("Creating MA plot...",stdout())
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	411
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	412 if(output_format_images == "pdf") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	413 pdf(output_MAplot)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	414 } else if(output_format_images == "svg") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	415 svg(output_MAplot)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	416 } else {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	417 ## png(output_MAplot)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	418 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	419
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	420 bitmap(output_MAplot,type="png16m",width=10.53,height=73)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	421 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	422
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	423 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
109 dfebd3787276 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 108 diff changeset	424 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red"))
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	425 abline(h=c(-1,1), col="blue")
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	426 dev.off()
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	427 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	428
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	429 if(output_PValue_distribution_plot != "/dev/null") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	430 write("Creating P-value distribution plot...",stdout())
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	431
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	432 if(output_format_images == "pdf") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	433 pdf(output_PValue_distribution_plot,width=14,height=14)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	434 } else if(output_format_images == "svg") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	435 svg(output_PValue_distribution_plot,width=14,height=14)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	436 } else {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	437 ## png(output_PValue_distribution_plot)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	438 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	439
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	440 bitmap(output_PValue_distribution_plot,type="png16m",width=73,height=73)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	441 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	442
109 dfebd3787276 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 108 diff changeset	443 expressed_genes <- subset(etable, PValue < 0.99)
dfebd3787276 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 108 diff changeset	444 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)")
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	445 center <- sum(h\$counts) / length(h\$counts)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	446 lines(c(0,1),c(center,center),lty=2,col="red",lwd=2)
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	447 k <- ksmooth(h\$mid, h\$counts)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	448 lines(k\$x,k\$y,col="red",lwd=2)
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	449 rmsd <- (h\$counts) - center
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	450 rmsd <- rmsd^2
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	451 rmsd <- sum(rmsd)
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	452 rmsd <- sqrt(rmsd)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	453 text(0,max(h\$counts),paste("e=",round(rmsd,2),sep=""),pos=4,col="blue")
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	454 ## change e into epsilon somehow
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	455 dev.off()
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	456 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	457 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	458
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	459 if(output_heatmap_plot != "/dev/null") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	460
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	461 if(output_format_images == "pdf") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	462 pdf(output_heatmap_plot,width=10.5)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	463 } else if(output_format_images == "svg") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	464 svg(output_heatmap_plot,width=10.5)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	465 } else {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	466 ## png(output_heatmap_plot)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	467 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	468
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	469 bitmap(output_heatmap_plot,type="png16m",width=10.53,height=73)
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	470 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	471
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	472 etable2 <- topTags(lrt, n=100)\$table
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	473 order <- rownames(etable2)
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	474 cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	475 heatmap(t(cpm_sub))
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	476 dev.off()
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	477 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	478
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	479 if(output_hierarchical_clustering_plot != "/dev/null") {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	480 if(output_hierarchical_clustering_plot == "pdf") {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	481 pdf(output_hierarchical_clustering_plot,width=10.5)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	482 } else if(output_hierarchical_clustering_plot == "svg") {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	483 svg(output_hierarchical_clustering_plot,width=10.5)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	484 } else {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	485 ## png(output_hierarchical_clustering_plot)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	486 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	487
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	488 bitmap(output_hierarchical_clustering_plot,type="png16m",width=10.53,height=73)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	489 }
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	490
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	491 mds_distance = as.dist(mds_distance_logFC\$distance.matrix)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	492 clustering = hclust(mds_distance)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	493 plot(clustering,main=paste("Cluster Dendogram on the ",mds_distance_logFC\$top," TopTags",sep="",sub="\ncomplete linkage on logFC MDS distance"))
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	494
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	495 dev.off()
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	496 }
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	497
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	498 if(output_RData_obj != "/dev/null") {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	499 save.image(output_RData_obj)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	500 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	501
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	502 write("Done!",stdout())
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	503 }
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	504 ]]>
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	505 </configfile>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	506 </configfiles>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	507
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	508 <inputs>
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	509 <conditional name="analysis_type">
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	510 <param name="analysis_select" type="select" label="Analysis type">
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	511 <option value="2_factor" selected="true">2-Group test</option>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	512 <option value="multi_factor">Multigroup test and/or complex designs with e.g. blocking</option>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	513 </param>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	514 <when value="2_factor">
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	515 <param name="factorLevel_control" type="text" value="Control"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	516 label="Specify a factor level" help="Only letters, numbers and underscores will be retained in this field">
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	517 <sanitizer>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	518 <valid initial="string.letters,string.digits"><add value="_" /></valid>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	519 </sanitizer>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	520 </param>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	521 <param name="countsFile_control" type="data" format="tabular,csv" multiple="true" label="Counts file(s)"/>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	522
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	523 <param name="factorLevel_condition" type="text" value="Condition"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	524 label="Specify a factor level" help="Only letters, numbers and underscores will be retained in this field">
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	525 <sanitizer>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	526 <valid initial="string.letters,string.digits"><add value="_" /></valid>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	527 </sanitizer>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	528 </param>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	529 <param name="countsFile_condition" type="data" format="tabular,csv" multiple="true" label="Counts file(s)"/>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	530 </when>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	531 <when value="multi_factor">
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	532 <param name="expression_matrix" type="data" format="tabular,csv" label="Expression (read count) matrix" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	533 <param name="design_matrix" type="data" format="tabular,csv" label="Design matrix"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	534 help="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from Expression matrix'." />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	535
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	536 <param name="contrast" type="text" label="Contrast (biological question)"
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	537 help="e.g. 'tumor-normal' or '(G1+G2)/2-G3' using the factors chosen in the design matrix. Read the 'makeContrasts' manual from Limma package for more info: http://www.bioconductor.org/packages/release/bioc/html/limma.html and http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf." />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	538 </when>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	539 </conditional>
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	540
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	541 <param name="analysis_report_genes" type="select" label="Report differentially expressed genes">
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	542 <option value="all" selected="true">All genes</option>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	543 <option value="significant">Only significant (defined by FDR cutoff)</option>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	544 </param>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	545
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	546 <param name="fdr" type="float" min="0" max="1" value="0.01" label="False Discovery Rate (FDR) cutoff" help="Used to highlight significant genes in figures" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	547
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	548 <param name="outputs" type="select" label="Optional desired outputs" multiple="true" display="checkboxes">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	549 <option value="make_output_raw_counts">Raw counts table</option>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	550 <option value="make_output_MDSplot_logFC">MDS-plot (logFC-method)</option>
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	551 <option value="make_output_MDSplot_logFC_coordinates">MDS-plot coordinates table (logFC-method)</option>
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	552 <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; slow)</option>
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	553 <option value="make_output_MDSplot_bcv_coordinates">MDS-plot coordinates table (BCV-method; slow)</option>
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	554 <option value="make_output_BCVplot">BCV-plot</option>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	555 <option value="make_output_MAplot">MA-plot</option>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	556 <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option>
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	557 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option>
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	558 <option value="make_output_heatmap_plot">Heatmap</option>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	559 <option value="make_output_RData_obj">R Data object</option>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	560 </param>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	561
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	562 <param name="output_format_images" type="select" label="Output format of images" display="radio">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	563 <option value="png">Portable network graphics (.png)</option>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	564 <option value="pdf">Portable document format (.pdf)</option>
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	565 <option value="svg" selected="true">Scalable vector graphics (.svg)</option>
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	566 </param>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	567 </inputs>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	568
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	569 <outputs>
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	570 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${on_string}: differentially expressed genes" >
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	571 <actions>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	572 <action name="column_names" type="metadata" default="original_gene_position,genes,logFC,logCPM,LR,PValue,FDR" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	573 </actions>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	574 </data>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	575 <data format="tabular" name="output_cpm" label="edgeR DGE on ${on_string}: CPM" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	576
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	577 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${on_string}: raw counts">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	578 <filter>outputs and ("make_output_raw_counts" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	579 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	580
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	581 <data format="png" name="output_MDSplot_logFC" label="edgeR DGE on ${on_string}: MDS-plot (logFC method)">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	582 <filter>outputs and ("make_output_MDSplot_logFC" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	583
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	584 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	585 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	586 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	587 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	588 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	589 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	590
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	591 <data format="tabular" name="output_MDSplot_logFC_coordinates" label="edgeR DGE on ${on_string}: MDS-plot coordinates table (logFC method)">
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	592 <filter>outputs and ("make_output_MDSplot_logFC_coordinates" in outputs)</filter>
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	593 </data>
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	594
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	595 <data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${on_string}: MDS-plot (bcv method)">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	596 <filter>outputs and ("make_output_MDSplot_bcv" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	597
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	598 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	599 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	600 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	601 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	602 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	603 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	604
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	605 <data format="tabular" name="output_MDSplot_bcv_coordinates" label="edgeR DGE on ${on_string}: MDS-plot coordinates table (BCV method)">
117 6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	606 <filter>outputs and ("make_output_MDSplot_bcv_coordinates" in outputs)</filter>
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	607 </data>
6df940f979c8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 116 diff changeset	608
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	609 <data format="png" name="output_BCVplot" label="edgeR DGE on ${on_string}: BCV-plot">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	610 <filter>outputs and ("make_output_BCVplot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	611
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	612 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	613 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	614 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	615 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	616 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	617 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	618
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	619 <data format="png" name="output_MAplot" label="edgeR DGE on ${on_string}: MA-plot">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	620 <filter>outputs and ("make_output_MAplot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	621
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	622 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	623 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	624 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	625 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	626 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	627 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	628
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	629 <data format="png" name="output_PValue_distribution_plot" label="edgeR DGE on ${on_string}: P-Value distribution">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	630 <filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	631
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	632 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	633 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	634 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	635 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	636 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	637 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	638
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	639 <data format="png" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${on_string}: Hierarchical custering">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	640 <filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	641
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	642 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	643 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	644 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	645 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	646 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	647 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	648
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	649 <data format="png" name="output_heatmap_plot" label="edgeR DGE on ${on_string}: Heatmap">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	650 <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	651
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	652 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	653 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	654 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	655 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	656 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	657 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	658
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	659 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${on_string}: R data object">
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	660 <filter>outputs and ("make_output_RData_obj" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	661 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	662
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	663 <data format="txt" name="output_R" label="edgeR DGE on ${on_string}: R output (debug)" >
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	664 <filter>outputs and ("make_output_R_stdout" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	665 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	666 </outputs>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	667
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	668 <tests>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	669 <test>
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	670 <param name="analysis_select" value="multi_factor" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	671
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	672 <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	673 <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.txt" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	674
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	675 <param name="contrast" value="E-C"/>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	676
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	677 <param name="analysis_report_genes" value="all"/>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	678 <param name="fdr" value="0.01" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	679
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	680 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	681 </test>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	682 <test>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	683 <param name="analysis_select" value="multi_factor" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	684
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	685 <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	686 <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.txt" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	687
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	688 <param name="contrast" value="E-C"/>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	689
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	690 <param name="analysis_report_genes" value="significant"/>
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	691 <param name="fdr" value="0.05" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	692
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	693 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	694 </test>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	695 <test>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	696 <param name="analysis_select" value="2_factor" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	697
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	698 <param name="factorLevel_control" value="C" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	699 <param name="countsFile_control" value="Differential_Gene_Expression/C1,Differential_Gene_Expression/C2,Differential_Gene_Expression/C3,Differential_Gene_Expression/C4" ftype="tabular" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	700
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	701 <param name="factorLevel_condition" value="E" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	702 <param name="countsFile_condition" value="Differential_Gene_Expression/E1,Differential_Gene_Expression/E2,Differential_Gene_Expression/E3,Differential_Gene_Expression/E4" ftype="tabular" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	703
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	704 <param name="analysis_report_genes" value="all"/>
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	705 <param name="fdr" value="0.01" />
5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	706
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	707 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	708 </test>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	709 <test>
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	710 <param name="analysis_select" value="2_factor" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	711
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	712 <param name="factorLevel_control" value="C" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	713 <param name="countsFile_control" value="Differential_Gene_Expression/C1,Differential_Gene_Expression/C2,Differential_Gene_Expression/C3,Differential_Gene_Expression/C4" ftype="tabular" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	714
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	715 <param name="factorLevel_condition" value="E" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	716 <param name="countsFile_condition" value="Differential_Gene_Expression/E1,Differential_Gene_Expression/E2,Differential_Gene_Expression/E3,Differential_Gene_Expression/E4" ftype="tabular" />
0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	717
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	718 <param name="analysis_report_genes" value="significant"/>
119 0a05f6a91d71 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit b3dcbc6b4e0510909aef9969da9941bed18599e6 yhoogstrate parents: 118 diff changeset	719 <param name="fdr" value="0.05" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	720
120 5c94a732bd62 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795 yhoogstrate parents: 119 diff changeset	721 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	722 </test>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	723 </tests>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	724
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	725 <help>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	726 edgeR: Differential Gene(Expression) Analysis
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	727 #############################################
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	728
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	729 Overview
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	730 --------
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	731 Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with other types of genome-scale count data [1].
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	732
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	733 For every experiment, the algorithm requires a design matrix. This matrix describes which samples belong to which groups.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	734 More details on this are given in the edgeR manual: http://www.bioconductor.org/packages/2.12/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	735 and the limma manual.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	736
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	737 Because the creation of a design matrix can be complex and time consuming, especially if no GUI is used, this package comes with an alternative tool which can help you with it.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	738 This tool is called edgeR Design Matrix Creator.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	739 If the appropriate design matrix (with corresponding links to the files) is given,
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	740 the correct contrast ( http://en.wikipedia.org/wiki/Contrast_(statistics) ) has to be given.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	741
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	742 If you have for example two groups, with an equal weight, you would like to compare either
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	743 "g1-g2" or "normal-cancer".
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	744
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	745 The test function makes use of a MCF7 dataset used in a study that indicates that a higher sequencing depth is not neccesairily more important than a higher amount of replaciates[2].
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	746
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	747 Input
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	748 -----
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	749 Expression matrix
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	750 ^^^^^^^^^^^^^^^^^
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	751 ::
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	752
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	753 Geneid "\t" Sample-1 "\t" Sample-2 "\t" Sample-3 "\t" Sample-4 [...] "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	754 SMURF "\t" 123 "\t" 21 "\t" 34545 "\t" 98 ... "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	755 BRCA1 "\t" 435 "\t" 6655 "\t" 45 "\t" 55 ... "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	756 LINK33 "\t" 4 "\t" 645 "\t" 345 "\t" 1 ... "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	757 SNORD78 "\t" 498 "\t" 65 "\t" 98 "\t" 27 ... "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	758 [...]
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	759
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	760 Note: Make sure the number of columns in the header is identical to the number of columns in the body.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	761
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	762 Design matrix
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	763 ^^^^^^^^^^^^^
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	764 ::
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	765
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	766 Sample "\t" Condition "\t" Ethnicity "\t" Patient "\t" Batch "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	767 Sample-1 "\t" Tumor "\t" European "\t" 1 "\t" 1 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	768 Sample-2 "\t" Normal "\t" European "\t" 1 "\t" 1 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	769 Sample-3 "\t" Tumor "\t" European "\t" 2 "\t" 1 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	770 Sample-4 "\t" Normal "\t" European "\t" 2 "\t" 1 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	771 Sample-5 "\t" Tumor "\t" African "\t" 3 "\t" 1 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	772 Sample-6 "\t" Normal "\t" African "\t" 3 "\t" 1 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	773 Sample-7 "\t" Tumor "\t" African "\t" 4 "\t" 2 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	774 Sample-8 "\t" Normal "\t" African "\t" 4 "\t" 2 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	775 Sample-9 "\t" Tumor "\t" Asian "\t" 5 "\t" 2 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	776 Sample-10 "\t" Normal "\t" Asian "\t" 5 "\t" 2 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	777 Sample-11 "\t" Tumor "\t" Asian "\t" 6 "\t" 2 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	778 Sample-12 "\t" Normal "\t" Asian "\t" 6 "\t" 2 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	779
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	780 Note: Avoid factor names that are (1) numerical, (2) contain mathematical symbols and preferebly only use letters.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	781
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	782 Contrast
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	783 ^^^^^^^^
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	784 The contrast represents the biological question. There can be many questions asked, e.g.:
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	785
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	786 - Tumor-Normal
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	787 - African-European
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	788 - 0.5*(Control+Placebo) / Treated
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	789
108 a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	790 @CONTACT@
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	791 </help>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	792
108 a02794bb9073 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 107 diff changeset	793 <expand macro="citations" />
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	794 </tool>

Mercurial > repos > yhoogstrate > edger_with_design_matrix

annotate edgeR_Differential_Gene_Expression.xml @ 120:5c94a732bd62 draft