edger_with_design_matrix: edgeR_Differential_Gene

annotate edgeR_Differential_Gene_Expression.xml @ 122:7bb87a6bc4d5 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc

author	yhoogstrate
date	Wed, 16 Dec 2015 11:15:18 -0500
parents	6c90a67a13fa
children

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]
121 6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	211
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	212 if(any(grepl("^[0-9]+$", old, perl=TRUE) == FALSE)){
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	213 # Convert invalid names
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	214 design_matrix[,i] <- make.names(design_matrix[,i])
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	215
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	216 # Print if names have been converted
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	217 if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	218 print("Renamed of factors:")
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	219 print(old)
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	220 print("To:")
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	221 print(design_matrix[,i])
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	222 }
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	223 } else {
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	224 # Only numerical factors: these are blocking / pairing factors
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	225 design_matrix[,i] <- as.numeric(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	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 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	228
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	229 ## 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	230 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	231 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	232 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	233
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	234 ## 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	235 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	236 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	237 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	238
f2ac9f6bc542 planemo 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 ## 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	240 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	241 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	242 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	243
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	244 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	245 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	246 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	247 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	248 }
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo 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 ## 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	252 ##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	253 ##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	254
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	255 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	256 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	257 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	258 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	259 } 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	260
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	261 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	262
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	263 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	264 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	265 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	266 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	267 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	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 # 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	270 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	271 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	272 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	273 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	274 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	275
f2ac9f6bc542 planemo 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 # 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	277 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	278 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	279 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	280 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	281 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	282 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	283 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	284 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	285
f2ac9f6bc542 planemo 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
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	287 # 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	288 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	289 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	290 n_dim <- nrow(dge\$samples)
122 7bb87a6bc4d5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc yhoogstrate parents: 121 diff changeset	291
7bb87a6bc4d5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc yhoogstrate parents: 121 diff changeset	292 if(n_dim >= nrow(dge\$counts)) {
7bb87a6bc4d5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc yhoogstrate parents: 121 diff changeset	293 n_dim <- 3
7bb87a6bc4d5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc yhoogstrate parents: 121 diff changeset	294 }
7bb87a6bc4d5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc yhoogstrate parents: 121 diff changeset	295
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	296 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	297 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	298
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	299 # 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	300 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	301 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	302
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	303 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	304 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	305 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	306 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	307 } 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	308 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	309 } 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	310 ## 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	311 ## 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	312
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	313 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	314 }
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	315
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	316 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	317 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	318 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	319 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	320 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	321 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	322
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 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	324 }
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	325
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	326 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	327 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	328 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	329 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	330 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	331 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	332 }
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	333 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	334
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	335
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	336 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	337 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	338
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	339 ## 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	340 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	341 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	342 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	343
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	344 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	345 ## 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	346 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	347 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	348 } 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	349 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	350 } 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	351 ## 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	352 ## 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	353
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	354 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	355 }
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	356
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	357 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	358 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	359 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	360 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	361 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	362 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	363
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	364 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	365 }
f2ac9f6bc542 planemo 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
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	367 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	368 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	369 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	370 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	371 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	372 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	373 }
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	374 }
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	376
f2ac9f6bc542 planemo 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 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	378 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	379
f2ac9f6bc542 planemo 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 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	381 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	382 } 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	383 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	384 } 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	385 ## 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	386 ## 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	387
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	388 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	389 }
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	391 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	392 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	393 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	394
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	395
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	396 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	397 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	398
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	399 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	400 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	401 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	402
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	403 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	404 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	405
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	406 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	407 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	408 }
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	409 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	410 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	411 }
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	412 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	413
f2ac9f6bc542 planemo 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 ## 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	415 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	416
f2ac9f6bc542 planemo 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 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	418 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	419 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	420
f2ac9f6bc542 planemo 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 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	422 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	423
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	424 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	425 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	426 } 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	427 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	428 } 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	429 ## 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	430 ## 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	431
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	432 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	433 }
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo 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 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	436 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	437 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	438 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	439 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	440
f2ac9f6bc542 planemo 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 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	442 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	443
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	444 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	445 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	446 } 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	447 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	448 } 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	449 ## 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	450 ## 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	451
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	452 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	453 }
f2ac9f6bc542 planemo 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
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	455 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	456 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	457 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	458 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	459 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	460 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	461 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	462 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	463 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	464 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	465 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	466 ## 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	467 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	468 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	469 }
f2ac9f6bc542 planemo 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 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	472
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	473 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	474 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	475 } 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	476 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	477 } 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	478 ## 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	479 ## 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	480
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	481 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	482 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	483
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	484 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	485 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	486 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	487 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	488 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	489 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	490
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	491 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	492 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	493 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	494 } 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	495 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	496 } 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	497 ## 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	498 ## 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	499
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	500 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	501 }
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	502
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	503 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	504 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	505 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	506
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	507 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	508 }
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	509
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	510 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	511 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	512 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	513
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	514 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	515 }
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	516 ]]>
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	517 </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	518 </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	519
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	520 <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	521 <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	522 <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	523 <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	524 <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	525 </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	526 <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	527 <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	528 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	529 <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	530 <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	531 </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	532 </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	533 <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	534
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 <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	536 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	537 <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	538 <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	539 </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	540 </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	541 <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	542 </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	543 <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	544 <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	545 <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	546 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	547
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	548 <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	549 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	550 </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	551 </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	552
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	553 <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	554 <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	555 <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	556 </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	557
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	558 <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	559
f2ac9f6bc542 planemo 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 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	561 <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	562 <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	563 <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	564 <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	565 <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	566 <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	567 <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	568 <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	569 <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	570 <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	571 <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	572 </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	573
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	574 <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	575 <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	576 <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	577 <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	578 </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	579 </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	580
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	581 <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	582 <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	583 <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	584 <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	585 </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	586 </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	587 <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	588
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	589 <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	590 <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	591 </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	592
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	593 <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	594 <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	595
f2ac9f6bc542 planemo 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 <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	597 <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	598 <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	599 <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	600 </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	601 </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	602
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	603 <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	604 <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	605 </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	606
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	607 <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	608 <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	609
f2ac9f6bc542 planemo 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 <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	611 <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	612 <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	613 <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	614 </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	615 </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	616
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	617 <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	618 <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	619 </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	620
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	621 <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	622 <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	623
f2ac9f6bc542 planemo 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 <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	625 <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	626 <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	627 <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	628 </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	629 </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	630
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	631 <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	632 <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	633
f2ac9f6bc542 planemo 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 <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	635 <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	636 <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	637 <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	638 </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	639 </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	640
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	641 <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	642 <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	643
f2ac9f6bc542 planemo 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 <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	645 <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	646 <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	647 <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	648 </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	649 </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	650
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	651 <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	652 <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	653
f2ac9f6bc542 planemo 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 <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	655 <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	656 <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	657 <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	658 </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	659 </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	660
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	661 <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	662 <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	663
f2ac9f6bc542 planemo 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 <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	665 <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	666 <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	667 <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	668 </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	669 </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	670
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	671 <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	672 <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	673 </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	674
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	675 <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	676 <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	677 </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	678 </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	679
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	680 <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	681 <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	682 <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	683
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	684 <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	685 <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	686
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	687 <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	688
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	689 <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	690 <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	691
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	692 <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	693 </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	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 <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	696
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 <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	698 <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	699
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 <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	701
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="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	703 <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	704
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	705 <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	706 </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	707 <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	708 <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	709
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	710 <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	711 <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	712
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	713 <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	714 <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	715
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	716 <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	717 <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	718
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 <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	720 </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	721 <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	722 <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	723
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	724 <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	725 <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	726
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	727 <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	728 <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	729
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	730 <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	731 <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	732
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	733 <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	734 </test>
121 6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	735 <test>
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	736 <param name="analysis_select" value="multi_factor" />
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	737
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	738 <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" />
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	739 <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.batch-effects.txt" />
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	740
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	741 <param name="contrast" value="E-C"/>
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	742
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	743 <param name="analysis_report_genes" value="all"/>
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	744 <param name="fdr" value="0.01" />
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	745
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	746 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.batch-effects.tabular.txt" />
6c90a67a13fa planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc yhoogstrate parents: 120 diff changeset	747 </test>
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	748 </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	749
f2ac9f6bc542 planemo 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 <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	751 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	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
f2ac9f6bc542 planemo 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 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	755 --------
f2ac9f6bc542 planemo 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 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	757
f2ac9f6bc542 planemo 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 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	759 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	760 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	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 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	763 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	764 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	765 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	766
f2ac9f6bc542 planemo 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 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	768 "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	769
f2ac9f6bc542 planemo 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 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	771
f2ac9f6bc542 planemo 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 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	773 -----
f2ac9f6bc542 planemo 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 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	775 ^^^^^^^^^^^^^^^^^
f2ac9f6bc542 planemo 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 ::
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo 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 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	779 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	780 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	781 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	782 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	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
f2ac9f6bc542 planemo 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 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	786
f2ac9f6bc542 planemo 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 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	788 ^^^^^^^^^^^^^
f2ac9f6bc542 planemo 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 ::
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	790
f2ac9f6bc542 planemo 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 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	792 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	793 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	794 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	795 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	796 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	797 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	798 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	799 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	800 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	801 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	802 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	803 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	804
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	805 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	806
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	807 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	808 ^^^^^^^^
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	809 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	810
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	811 - 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	812 - 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	813 - 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	814
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	815 @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	816 </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	817
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	818 <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	819 </tool>

Mercurial > repos > yhoogstrate > edger_with_design_matrix

annotate edgeR_Differential_Gene_Expression.xml @ 122:7bb87a6bc4d5 draft