edger_with_design_matrix: edgeR_Differential_Gene

annotate edgeR_Differential_Gene_Expression.xml @ 4:5d38abf7e4b6 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 10:43:03 -0500
parents	12fb0d4b1e93
children	bde663b872d9

rev	line source
1 a4a4c88783ea planemo 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"?>
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.b">
1 a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	5 <macros>
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	6 <import>edgeR_macros.xml</import>
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	7 </macros>
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	8
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	15 source="both"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	16 level="fatal"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	17 description="Have the design- and expression-matrix been swapped?" />
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	18 <regex match="Error in eval$expr, envir, enclos$"
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	19 source="both"
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	20 level="fatal"
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	21 description="You have most likely used a condition in the contrast, that is not present in the Design matrix" />
1 a4a4c88783ea planemo 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"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	23 source="both"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	24 level="fatal" />
a4a4c88783ea planemo 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"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	26 source="stderr"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	27 level="log" />
a4a4c88783ea planemo 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"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	29 source="stderr"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	30 level="log" />
a4a4c88783ea planemo 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"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	32 source="stderr"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	33 level="warning"
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	34 description="LOCALE has not been set correctly" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 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>
1 a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 -->
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	64 #if $output_MDSplot_logFC_coordinates:
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	65 $output_MDSplot_logFC_coordinates
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	66 #else:
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	67 /dev/null
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	68 #end if
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	69
1 a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	76 #if $output_MDSplot_bcv_coordinates:
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	77 $output_MDSplot_bcv_coordinates
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	78 #else:
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	79 /dev/null
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	80 #end if
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	81
1 a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 '
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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">
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	124 <![CDATA[
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	125
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	126 library(limma,quietly=TRUE) ## quietly to avoid unnecessaity stderr messages
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	127 library(edgeR,quietly=TRUE) ## quietly to avoid unnecessaity stderr messages
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	128 library(splines,quietly=TRUE)## quietly to avoid unnecessaity stderr messages
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	131 args <- commandArgs(trailingOnly = TRUE)
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	133 expression_matrix_file <- args[1]
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	134 design_matrix_file <- args[2]
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	135 contrast <- args[3]
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	137 fdr <- args[4]
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	139 output_count_edgeR <- args[5]
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	140 output_cpm <- args[6]
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	142 output_xpkm <- args[7] ##FPKM file - to be implemented
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	144 output_raw_counts <- args[8]
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	145
1 a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	146 output_MDSplot_logFC <- args[9]
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	147 output_MDSplot_logFC_coordinates <- args[10]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	148
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	149 output_MDSplot_bcv <- args[11]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	150 output_MDSplot_bcv_coordinates <- args[12]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	151
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	152 output_BCVplot <- args[13]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	153 output_MAplot <- args[14]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	154 output_PValue_distribution_plot <- args[15]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	155 output_hierarchical_clustering_plot <- args[16]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	156 output_heatmap_plot <- args[17]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	157 output_RData_obj <- args[18]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	158 output_format_images <- args[19]
1 a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	162 expression_matrix <- read.delim(expression_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	163 design_matrix <- read.delim(design_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	165 colnames(design_matrix) <- make.names(colnames(design_matrix))
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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)) {
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	168 old <- design_matrix[,i]
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	169 design_matrix[,i] <- make.names(design_matrix[,i])
a4a4c88783ea planemo 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")) {
a4a4c88783ea planemo 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:")
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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:")
a4a4c88783ea planemo 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])
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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:
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	177 ##design_matrix[,i] <- as.factor(design_matrix[,i])
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	181 columns <- match(rownames(design_matrix),colnames(expression_matrix))
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	182 columns <- columns[!is.na(columns)]
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	183 read_counts <- expression_matrix[,columns]
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	186 columns <- match(colnames(read_counts),rownames(design_matrix))
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	187 columns <- columns[!is.na(columns)]
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	188 design_matrix <- design_matrix[columns,,drop=FALSE]
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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:
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	191 exclude_HTSeq <- c("no_feature","ambiguous","too_low_aQual","not_aligned","alignment_not_unique")
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	192 exclude_DEXSeq <- c("_ambiguous","_empty","_lowaqual","_notaligned")
4 5d38abf7e4b6 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit e42aebc7a9b64744919668cb9a856b5df8a61387 yhoogstrate parents: 3 diff changeset	193 exclude_STAR <- c("N_unmapped", "N_multimapping", "N_noFeature", "N_ambiguous")
1 a4a4c88783ea planemo 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
4 5d38abf7e4b6 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit e42aebc7a9b64744919668cb9a856b5df8a61387 yhoogstrate parents: 3 diff changeset	195 exclude <- match(c(exclude_HTSeq, exclude_DEXSeq, exclude_STAR),rownames(read_counts))
1 a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	196 exclude <- exclude[is.na(exclude)==0]
a4a4c88783ea planemo 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) {
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	198 read_counts <- read_counts[-exclude,]
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	203 ##order <- match(colnames(read_counts) , rownames(design_matrix))
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	204 ##read_counts_ordered <- read_counts[,order2]
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	206 empty_samples <- apply(read_counts,2,function(x) sum(x) == 0)
a4a4c88783ea planemo 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) {
a4a4c88783ea planemo 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())
a4a4c88783ea planemo 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())
a4a4c88783ea planemo 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 {
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	212 dge <- DGEList(counts=read_counts,genes=rownames(read_counts))
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	214 formula <- paste(c("~0",make.names(colnames(design_matrix))),collapse = " + ")
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	215 design_matrix_tmp <- design_matrix
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	216 colnames(design_matrix_tmp) <- make.names(colnames(design_matrix_tmp))
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	217 design <- model.matrix(as.formula(formula),design_matrix_tmp)
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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")]
a4a4c88783ea planemo 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))
a4a4c88783ea planemo 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)))
a4a4c88783ea planemo 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]
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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())
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	229 dge <- calcNormFactors(dge)
a4a4c88783ea planemo 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())
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	231 dge <- estimateGLMCommonDisp(dge,design)
a4a4c88783ea planemo 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())
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	233 dge <- estimateGLMTrendedDisp(dge,design)
a4a4c88783ea planemo 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())
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	235 dge <- estimateGLMTagwiseDisp(dge,design)
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	238 # hierarchical clustering makes use of the distance of the MDS
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	239 if(output_MDSplot_logFC != "/dev/null" \|\| output_MDSplot_logFC_coordinates != "/dev/null" \|\| output_hierarchical_clustering_plot != "/dev/null") {
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	240 write("Calculating MDS plot (logFC method)",stdout())
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	241 n_dim <- nrow(dge\$samples)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 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))
1 a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	245 # Reset to primary dimensions
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	246 mds_distance_logFC\$x = mds_distance_logFC\$cmdscale.out[,1]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	247 mds_distance_logFC\$y = mds_distance_logFC\$cmdscale.out[,2]
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	248
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	249 if(output_MDSplot_logFC != "/dev/null") {
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	250 write("Creating MDS plot (logFC method)",stdout())
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	251 if(output_format_images == "pdf") {
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	252 pdf(output_MDSplot_logFC,height=14,width=14)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	253 } else if(output_format_images == "svg") {
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	254 svg(output_MDSplot_logFC,height=14,width=14)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	255 } else {
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	256 ## png(output_MDSplot_logFC)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 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/
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	258
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	259 bitmap(output_MDSplot_logFC,type="png16m",height=73,width=73)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	260 }
1 a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	262 diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x))
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	263 diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y))
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 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")
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	265 points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	266 text(mds_distance_logFC\$x,mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	267 rm(diff_x,diff_y)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	268
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	269 dev.off()
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	270 }
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	271
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	272 if(output_MDSplot_logFC_coordinates != "/dev/null") {
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	273 n_dim <- ncol(mds_distance_logFC\$cmdscale.out)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	274 colnames(mds_distance_logFC\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_")
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	275 export <- data.frame(samples=rownames(mds_distance_logFC\$cmdscale.out),mds_distance_logFC\$cmdscale.out)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	276 row.names(export) <- NULL
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	277 write.table(file=output_MDSplot_logFC_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	278 }
1 a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	281
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	282 if(output_MDSplot_bcv != "/dev/null" \|\| output_MDSplot_bcv_coordinates != "/dev/null" ) {
1 a4a4c88783ea planemo 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())
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	286 n_dim <- nrow(dge\$samples)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 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))
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	288 dev.off()
1 a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	290 if(output_MDSplot_logFC != "/dev/null") {
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	291 ## 2. Re-plot the coordinates in a new figure with the size and settings.
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	292 if(output_format_images == "pdf") {
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	293 pdf(output_MDSplot_bcv,height=14,width=14)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	294 } else if(output_format_images == "svg") {
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	295 svg(output_MDSplot_bcv,height=14,width=14)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	296 } else {
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	297 ## png(output_MDSplot_bcv)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 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/
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	299
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	300 bitmap(output_MDSplot_bcv,type="png16m",height=73,width=73)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	301 }
1 a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	303 diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	304 diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 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")
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	306 points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	307 text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	308 rm(diff_x,diff_y)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	309
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	310 dev.off()
1 a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	313 if(output_MDSplot_bcv_coordinates != "/dev/null") {
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	314 n_dim <- ncol(mds_distance_BCV\$cmdscale.out)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	315 colnames(mds_distance_BCV\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_")
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	316 export <- data.frame(samples=rownames(mds_distance_BCV\$cmdscale.out),mds_distance_BCV\$cmdscale.out)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	317 row.names(export) <- NULL
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	318 write.table(file=output_MDSplot_bcv_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE)
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	319 }
1 a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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())
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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 {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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/
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	334 bitmap(output_BCVplot,type="png16m",width=10.53,height=73)
1 a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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")
a4a4c88783ea planemo 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()
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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())
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	343 fit <- glmFit(dge,design)
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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())
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	346 cont <- c(contrast)
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	347 cont <- makeContrasts(contrasts=cont, levels=design)
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	349 lrt <- glmLRT(fit, contrast=cont[,1])
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	350 write(paste("Exporting DGE results to file...",output_count_edgeR,sep=""),stdout())
1 a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	358 etable <- topTags(lrt, n=nrow(dge))\$table
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	359 etable <- etable[order(etable\$FDR), ]
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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())
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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 {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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/
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	372 bitmap(output_MAplot,type="png16m",width=10.53,height=73)
1 a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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"))
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	376 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red"))
a4a4c88783ea planemo 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")
a4a4c88783ea planemo 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()
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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())
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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 {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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/
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	392 bitmap(output_PValue_distribution_plot,type="png16m",width=73,height=73)
1 a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	395 expressed_genes <- subset(etable, PValue < 0.99)
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	396 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)")
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	397 center <- sum(h\$counts) / length(h\$counts)
a4a4c88783ea planemo 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)
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	399 k <- ksmooth(h\$mid, h\$counts)
a4a4c88783ea planemo 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)
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	401 rmsd <- (h\$counts) - center
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	402 rmsd <- rmsd^2
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	403 rmsd <- sum(rmsd)
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	404 rmsd <- sqrt(rmsd)
a4a4c88783ea planemo 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")
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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()
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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 {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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/
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	421 bitmap(output_heatmap_plot,type="png16m",width=10.53,height=73)
1 a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	424 etable2 <- topTags(lrt, n=100)\$table
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	425 order <- rownames(etable2)
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	426 cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
a4a4c88783ea planemo 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))
a4a4c88783ea planemo 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()
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	431 if(output_hierarchical_clustering_plot != "/dev/null") {
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	432 if(output_hierarchical_clustering_plot == "pdf") {
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	433 pdf(output_hierarchical_clustering_plot,width=10.5)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	434 } else if(output_hierarchical_clustering_plot == "svg") {
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	435 svg(output_hierarchical_clustering_plot,width=10.5)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	436 } else {
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	437 ## png(output_hierarchical_clustering_plot)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 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/
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	439
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	440 bitmap(output_hierarchical_clustering_plot,type="png16m",width=10.53,height=73)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	441 }
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	442
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	443 mds_distance = as.dist(mds_distance_logFC\$distance.matrix)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	444 clustering = hclust(mds_distance)
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	445 plot(clustering,main=paste("Cluster Dendogram on the ",mds_distance_logFC\$top," TopTags",sep="",sub="\ncomplete linkage on logFC MDS distance"))
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	446
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	447 dev.off()
ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	448 }
1 a4a4c88783ea planemo 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
a4a4c88783ea planemo 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") {
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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())
a4a4c88783ea planemo 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 }
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	456 ]]>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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'." />
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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." />
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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)" />
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	471 <option value="make_output_MDSplot_logFC_coordinates">MDS-plot coordinates table (logFC-method)</option>
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	472 <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; slow)</option>
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	473 <option value="make_output_MDSplot_bcv_coordinates">MDS-plot coordinates table (BCV-method; slow)</option>
1 a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	477 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option>
1 a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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)">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 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)">
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	508 <filter>outputs and ("make_output_MDSplot_logFC_coordinates" in outputs)</filter>
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	509 </data>
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	510
1 a4a4c88783ea planemo 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)">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
3 12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 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)">
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	522 <filter>outputs and ("make_output_MDSplot_bcv_coordinates" in outputs)</filter>
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	523 </data>
12fb0d4b1e93 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f yhoogstrate parents: 2 diff changeset	524
1 a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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">
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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)" >
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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"/>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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" />
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 #############################################
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 --------
a4a4c88783ea planemo 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].
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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.
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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.
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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.
a4a4c88783ea planemo 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.
a4a4c88783ea planemo 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,
a4a4c88783ea planemo 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.
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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".
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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].
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 -----
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 ^^^^^^^^^^^^^^^^^
a4a4c88783ea planemo 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 ::
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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 [...]
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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.
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 ^^^^^^^^^^^^^
a4a4c88783ea planemo 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 ::
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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"
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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.
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 ^^^^^^^^
a4a4c88783ea planemo 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.:
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 ------------
a4a4c88783ea planemo 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
2 ec951a5017f8 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be yhoogstrate parents: 1 diff changeset	667 This tool requires no specific configuration. The following dependencies will installed automatically:
1 a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	670 - limma
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	671 - edgeR
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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 -------
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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
a4a4c88783ea planemo 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)
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	682 @CONTACT@
a4a4c88783ea planemo 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>
a4a4c88783ea planemo 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
a4a4c88783ea planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty yhoogstrate parents: diff changeset	685 <expand macro="citations" />
a4a4c88783ea planemo 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 @ 4:5d38abf7e4b6 draft