edger_with_design_matrix: edgeR_Differential_Gene

annotate edgeR_Differential_Gene_Expression.xml @ 118:7e98e8bcfbf7 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit e42aebc7a9b64744919668cb9a856b5df8a61387

author	yhoogstrate
date	Wed, 09 Dec 2015 10:42:33 -0500
parents	6df940f979c8
children	0a05f6a91d71

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
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	39 <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	40 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	41 $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	42 $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	43 $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	44
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	45 $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	46
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	47 $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	48 $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	49
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	50 /dev/null <!-- Calculation of FPKM/RPKM should come here -->
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	51
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	52 #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	53 $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	54 #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	55 /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	56 #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	57
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	58 #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	59 $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	60 #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	61 /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	62 #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	63
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	64 #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	65 $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	66 #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	67 /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	68 #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	69
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	70 #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	71 $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	72 #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	73 /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	74 #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	75
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	76 #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	77 $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	78 #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	79 /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	80 #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	81
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	82 #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	83 $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	84 #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	85 /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	86 #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	87
f2ac9f6bc542 planemo 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 #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	89 $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	90 #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	91 /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	92 #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	93
f2ac9f6bc542 planemo 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 #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	95 $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	96 #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	97 /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	98 #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	99
f2ac9f6bc542 planemo 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 #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	101 $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	102 #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	103 /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	104 #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	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	106 #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	107 $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	108 #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	109 /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	110 #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	111
f2ac9f6bc542 planemo 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 #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	113 $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	114 #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	115 /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	116 #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	117
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	118 $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	119 '
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	120 </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	121
f2ac9f6bc542 planemo 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 <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	123 <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	124 <![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	125
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	126 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	127 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	128 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	129
f2ac9f6bc542 planemo 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 ## 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	131 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	132
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	133 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	134 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	135 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	136
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	137 fdr <- args[4]
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	138
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	139 output_count_edgeR <- args[5]
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	140 output_cpm <- args[6]
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	141
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	142 output_xpkm <- args[7] ##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	143
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	144 output_raw_counts <- args[8]
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	145
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	146 output_MDSplot_logFC <- 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	147 output_MDSplot_logFC_coordinates <- args[10]
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	148
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	149 output_MDSplot_bcv <- args[11]
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	150 output_MDSplot_bcv_coordinates <- args[12]
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	151
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	152 output_BCVplot <- args[13]
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	153 output_MAplot <- args[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	154 output_PValue_distribution_plot <- args[15]
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	155 output_hierarchical_clustering_plot <- args[16]
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	156 output_heatmap_plot <- args[17]
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	157 output_RData_obj <- args[18]
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	158 output_format_images <- args[19]
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	159
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	160
f2ac9f6bc542 planemo 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 ## 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	162 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	163 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	164
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 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	166
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	167 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	168 old <- design_matrix[,i]
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	169 design_matrix[,i] <- make.names(design_matrix[,i])
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	170 if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	171 print("Renaming of factors:")
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	172 print(old)
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	173 print("To:")
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	174 print(design_matrix[,i])
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	175 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	176 ## The following line seems to malfunction the script:
107 049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: 105 diff changeset	177 ##design_matrix[,i] <- as.factor(design_matrix[,i])
105 f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	178 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	179
f2ac9f6bc542 planemo 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 ## 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	181 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	182 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	183 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	184
f2ac9f6bc542 planemo 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 ## 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	186 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	187 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	188 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	189
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	190 ## 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	191 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	192 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	193 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	194
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	195 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	196 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	197 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	198 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	199 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	200
f2ac9f6bc542 planemo 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 ## 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	203 ##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	204 ##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	205
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	206 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	207 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	208 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	209 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	210 } 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	211
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	212 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	213
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	214 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	215 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	216 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	217 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	218 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	219
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	220 # 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	221 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	222 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	223 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	224 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	225 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	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 # 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	228 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	229 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	230 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	231 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	232 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	233 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	234 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	235 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	236
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	237
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	238 # 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	239 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	240 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	241 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	242 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	243 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	244
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	245 # 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	246 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	247 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	248
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	249 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	250 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	251 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	252 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	253 } 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	254 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	255 } 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	256 ## 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	257 ## 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	258
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	259 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	260 }
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	261
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	262 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	263 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	264 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	265 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	266 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	267 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	268
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	269 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	270 }
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	271
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	272 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	273 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	274 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	275 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	276 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	277 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	278 }
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 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	280
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	281
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	282 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	283 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	284
f2ac9f6bc542 planemo 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 ## 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	286 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	287 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	288 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	289
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 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	291 ## 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	292 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	293 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	294 } 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	295 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	296 } 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	297 ## 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	298 ## 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	299
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 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	301 }
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	302
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	303 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	304 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	305 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	306 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	307 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	308 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	309
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	310 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	311 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	312
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	313 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	314 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	315 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	316 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	317 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	318 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	319 }
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	320 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	321
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	322
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	323 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	324 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	325
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	326 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	327 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	328 } 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	329 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	330 } 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	331 ## 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	332 ## 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	333
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	334 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	335 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	336
f2ac9f6bc542 planemo 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 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	338 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	339 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	340
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	341
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	342 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	343 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	344
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	345 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	346 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	347 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	348
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	349 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	350 write(paste("Exporting DGE results to file...",output_count_edgeR,sep=""),stdout())
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	351 write.table(file=output_count_edgeR,topTags(lrt,n=nrow(read_counts))\$table,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	352 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	353
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	354 ## 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	355 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	356
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	357 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	358 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	359 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	360
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	361 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	362 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	363
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	364 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	365 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	366 } 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	367 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	368 } 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	369 ## 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	370 ## 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	371
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	372 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	373 }
f2ac9f6bc542 planemo 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 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	376 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	377 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	378 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	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
f2ac9f6bc542 planemo 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 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	382 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	383
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	384 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	385 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	386 } 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	387 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	388 } 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	389 ## 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	390 ## 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	391
111 b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	392 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	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
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	395 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	396 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	397 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	398 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	399 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	400 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	401 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	402 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	403 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	404 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	405 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	406 ## 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	407 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	408 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	409 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	410
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	411 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	412
f2ac9f6bc542 planemo 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 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	414 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	415 } 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	416 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	417 } 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	418 ## 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	419 ## 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	420
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	421 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	422 }
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	423
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	424 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	425 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	426 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	427 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	428 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	429 }
f2ac9f6bc542 planemo 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
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	431 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	432 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	433 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	434 } 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	435 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	436 } 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	437 ## 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	438 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
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	439
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689 yhoogstrate parents: 110 diff changeset	440 bitmap(output_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	441 }
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	442
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	443 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	444 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	445 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	446
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	447 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	448 }
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	449
f2ac9f6bc542 planemo 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 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	451 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	452 }
f2ac9f6bc542 planemo 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 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	455 }
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	456 ]]>
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	457 </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	458 </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	459
f2ac9f6bc542 planemo 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 <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	461 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) 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	462 <param name="design_matrix" type="data" format="tabular" label="Design matrix" help="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from 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	463
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	464 <param name="contrast" type="text" label="Contrast (biological question)" 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." />
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo 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 <param name="fdr" type="float" min="0" max="1" value="0.05" label="False Discovery Rate (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	467
f2ac9f6bc542 planemo 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 <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	469 <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	470 <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	471 <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	472 <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	473 <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	474 <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	475 <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	476 <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	477 <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	478 <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	479 <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	480 </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	481
f2ac9f6bc542 planemo 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 <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	483 <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	484 <option value="pdf">Portable document format (.pdf)</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	485 <option value="svg">Scalable vector graphics (.svg)</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	486 </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	487 </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	488
f2ac9f6bc542 planemo 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 <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	490 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differentially expressed genes" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	491 <data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - 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	492
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	493 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - 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	494 <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	495 </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	496
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	497 <data format="png" name="output_MDSplot_logFC" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (logFC method)">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	498 <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	499
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	500 <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	501 <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	502 <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	503 <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	504 </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	505 </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	506
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	507 <data format="tabular" name="output_MDSplot_logFC_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (logFC method)">
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	508 <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	509 </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	510
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	511 <data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (bcv method)">
f2ac9f6bc542 planemo 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 <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	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 <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	515 <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	516 <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	517 <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	518 </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	519 </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	520
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	521 <data format="tabular" name="output_MDSplot_bcv_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (BCV method)">
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	522 <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	523 </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	524
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	525 <data format="png" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-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	526 <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	527
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	528 <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	529 <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	530 <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	531 <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	532 </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	533 </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	534
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	535 <data format="png" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-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	536 <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	537
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	538 <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	539 <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	540 <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	541 <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	542 </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	543 </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	544
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	545 <data format="png" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	546 <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	547
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	548 <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	549 <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	550 <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	551 <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	552 </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	553 </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	554
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	555 <data format="png" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	556 <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	557
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	558 <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	559 <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	560 <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	561 <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	562 </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	563 </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	564
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	565 <data format="png" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
f2ac9f6bc542 planemo 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 <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	567
f2ac9f6bc542 planemo 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 <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	569 <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	570 <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	571 <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	572 </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	573 </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	574
f2ac9f6bc542 planemo 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 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object">
f2ac9f6bc542 planemo 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 <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	577 </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	578
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	579 <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" >
f2ac9f6bc542 planemo 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 <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	581 </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	582 </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	583
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	584 <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	585 <test>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	586 <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	587 <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	588
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	589 <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	590
f2ac9f6bc542 planemo 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 <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	592
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	593 <param name="output_format_images" value="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	594
f2ac9f6bc542 planemo 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 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.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	596 </test>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	597 </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	598
f2ac9f6bc542 planemo 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 <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	600 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	601 #############################################
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	603 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	604 --------
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	605 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	606
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	607 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	608 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	609 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	610
f2ac9f6bc542 planemo 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 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	612 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	613 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	614 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	615
f2ac9f6bc542 planemo 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 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	617 "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	618
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	619 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	620
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	621 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	622 -----
f2ac9f6bc542 planemo 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 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	624 ^^^^^^^^^^^^^^^^^
f2ac9f6bc542 planemo 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 ::
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo 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 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	628 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	629 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	630 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	631 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	632 [...]
f2ac9f6bc542 planemo 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 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	635
f2ac9f6bc542 planemo 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 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	637 ^^^^^^^^^^^^^
f2ac9f6bc542 planemo 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 ::
f2ac9f6bc542 planemo 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
f2ac9f6bc542 planemo 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 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	641 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	642 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	643 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	644 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	645 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	646 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	647 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	648 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	649 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	650 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	651 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	652 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	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 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	655
f2ac9f6bc542 planemo 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 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	657 ^^^^^^^^
f2ac9f6bc542 planemo 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 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	659
f2ac9f6bc542 planemo 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 - 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	661 - 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	662 - 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	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 Installation
f2ac9f6bc542 planemo 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 ------------
f2ac9f6bc542 planemo 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
116 ed809072dc95 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty yhoogstrate parents: 115 diff changeset	667 This tool requires no specific configuration. The following dependencies will installed automatically:
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	668
f2ac9f6bc542 planemo 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 - R
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	670 - limma
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	671 - edgeR
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
f2ac9f6bc542 planemo 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 License
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	674 -------
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	675 - R
f2ac9f6bc542 planemo 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 - GPL 2 & GPL 3
f2ac9f6bc542 planemo 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 - limma
f2ac9f6bc542 planemo 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 - GPL (>=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	679 - 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	680 - GPL (>=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	681
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	682 @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	683 </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	684
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	685 <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	686 </tool>

Mercurial > repos > yhoogstrate > edger_with_design_matrix

annotate edgeR_Differential_Gene_Expression.xml @ 118:7e98e8bcfbf7 draft