# HG changeset patch # User yhoogstrate # Date 1441097124 14400 # Node ID a02794bb9073251b4186f9b941b18cbda3ccab3a # Parent 049d8bc2214e600c9039e5b288cc3cf851ffa658 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty diff -r 049d8bc2214e -r a02794bb9073 edgeR_Concatenate_Expression_Matrices.xml --- a/edgeR_Concatenate_Expression_Matrices.xml Tue Sep 01 04:32:16 2015 -0400 +++ b/edgeR_Concatenate_Expression_Matrices.xml Tue Sep 01 04:45:24 2015 -0400 @@ -1,168 +1,172 @@ - Create a full expression matrix by selecting the desired columns from specific count tables - - - #set $j = 0 - #set $paste = [] - - #if $add_geneids.choice == "true": - #set $filename = str($j)+".txt" - #set paste = paste + [$filename] - - cut -f $add_geneids.column_geneids.value "$add_geneids.sample_geneids" > $filename ; - #set $j += 1 - #end if - - #for $sample in $samples: - ##echo "$sample.column_index" - ##echo "$sample.column_index.value" - - #set $column_str = ",".join([str(x).strip() for x in $sample.column_index.value]) - #set $filename = str($j)+".txt" - #set paste = paste + [$filename] - - cut -f "$column_str" "$sample.sample" > $filename ; - #set $j += 1 - #end for - - #if $add_lengths.choice == "true": - #set $filename = str($j)+".txt" - #set paste = paste + [$filename] - - cut -f $add_lengths.column_lengths.value "$add_lengths.sample_lengths" > $filename ; - #set $j += 1 - #end if - - #set $paste_str = " ".join([str(x).strip() for x in $paste]) - - paste $paste_str > $expression_matrix - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create a full expression matrix by selecting the desired columns from specific count tables + + + edgeR_macros.xml + + + + #set $j = 0 + #set $paste = [] + + #if $add_geneids.choice == "true": + #set $filename = str($j)+".txt" + #set paste = paste + [$filename] + + cut -f $add_geneids.column_geneids.value "$add_geneids.sample_geneids" > $filename ; + #set $j += 1 + #end if + + #for $sample in $samples: + ##echo "$sample.column_index" + ##echo "$sample.column_index.value" + + #set $column_str = ",".join([str(x).strip() for x in $sample.column_index.value]) + #set $filename = str($j)+".txt" + #set paste = paste + [$filename] + + cut -f "$column_str" "$sample.sample" > $filename ; + #set $j += 1 + #end for + + #if $add_lengths.choice == "true": + #set $filename = str($j)+".txt" + #set paste = paste + [$filename] + + cut -f $add_lengths.column_lengths.value "$add_lengths.sample_lengths" > $filename ; + #set $j += 1 + #end if + + #set $paste_str = " ".join([str(x).strip() for x in $paste]) + + paste $paste_str > $expression_matrix + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + edgeR: Concatenate Expression Matrices ####################################### @@ -179,28 +183,8 @@ Input ----- - -Contact -------- - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.dtls.nl/ - -http://toolshed.g2.bx.psu.edu - -http://testtoolshed.g2.bx.psu.edu/ - - - - 10.1093/bioinformatics/btp616 - 10.1093/bioinformatics/btt688 - +@CONTACT@ + + + diff -r 049d8bc2214e -r a02794bb9073 edgeR_Convert_DGE_Table_to_Bedgraph.xml --- a/edgeR_Convert_DGE_Table_to_Bedgraph.xml Tue Sep 01 04:32:16 2015 -0400 +++ b/edgeR_Convert_DGE_Table_to_Bedgraph.xml Tue Sep 01 04:45:24 2015 -0400 @@ -1,90 +1,93 @@ - - EdgeR's "differentially expressed genes" table to bedgraph(s) - - - edger_dge_table_to_bedgraph - - - - edger_dge_table_to_bedgraph - -t $cpm_table - -g $geneset - - #if $logfc: - -c3 $logfc - #end if - - #if $logcpm: - -c4 $logcpm - #end if - - #if $lr: - -c5 $lr - #end if - - #if $pvalue: - -c6 $pvalue - #end if - - #if $fdr: - -c7 $fdr - #end if - - - - - - - - - - - - - - - - - - "c3" in columns - - - - "c4" in columns - - - - "c5" in columns - - - - "c6" in columns - - - - "c7" in columns - - - - - - - - - - - - - - - - - P-values and FDRs are swapped from 1 to 0, and 0 to 1, because this way the most siginificant genes will obtain the highest values which is convenient for visualisation. - - - - 10.1093/bioinformatics/btp616 - 10.1093/bioinformatics/btt688 - + + EdgeR's "differentially expressed genes" table to bedgraph(s) + + + edgeR_macros.xml + + + + edger_dge_table_to_bedgraph + + + + edger_dge_table_to_bedgraph + -t $cpm_table + -g $geneset + + #if $logfc: + -c3 $logfc + #end if + + #if $logcpm: + -c4 $logcpm + #end if + + #if $lr: + -c5 $lr + #end if + + #if $pvalue: + -c6 $pvalue + #end if + + #if $fdr: + -c7 $fdr + #end if + + + + + + + + + + + + + + + + + + "c3" in columns + + + + "c4" in columns + + + + "c5" in columns + + + + "c6" in columns + + + + "c7" in columns + + + + + + + + + + + + + + + + + P-values and FDRs are swapped from 1 to 0, and 0 to 1, because this way the most siginificant genes will obtain the highest values which is convenient for visualisation. + + @CONTACT@ + + + diff -r 049d8bc2214e -r a02794bb9073 edgeR_Design_from_Expression_Matrix.xml --- a/edgeR_Design_from_Expression_Matrix.xml Tue Sep 01 04:32:16 2015 -0400 +++ b/edgeR_Design_from_Expression_Matrix.xml Tue Sep 01 04:45:24 2015 -0400 @@ -1,119 +1,123 @@ - Create design- from an expression matrix - - - design_matrix_creator - - - - design_matrix_creator - -c $expression_matrix - - #set $unique_columns = [] - #for $factor in $treatments: - #for $level in $factor.rep_factorLevel: - #for $val in $level.factorIndex.value: - #if str($val) not in $unique_columns: - #set $unique_columns = $unique_columns + [str($val)] - #end if - #end for - #end for - #end for - - #set $unique_columns = " ".join(unique_columns) - -s $unique_columns - - -t - #for $factor in $treatments: - #set $factor_str = str($factor.name).encode('base64').replace('\n','') - - #for $level in $factor.rep_factorLevel: - #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value]) - #end for - - $factor_str - #end for - - #if $choose_blocking.choice == "true" - -b - #for blocking in $choose_blocking.blocking_repeat: - #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','') - - #for $block_iter in $blocking.block: - #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value]) - #set $blocking_str = $blocking_str+":"+$block_str - #end for - - $blocking_str - #end for - #end if - - -o $design_matrix - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Create design- from an expression matrix + + + edgeR_macros.xml + + + + design_matrix_creator + + + + design_matrix_creator + -c $expression_matrix + + #set $unique_columns = [] + #for $factor in $treatments: + #for $level in $factor.rep_factorLevel: + #for $val in $level.factorIndex.value: + #if str($val) not in $unique_columns: + #set $unique_columns = $unique_columns + [str($val)] + #end if + #end for + #end for + #end for + + #set $unique_columns = " ".join(unique_columns) + -s $unique_columns + + -t + #for $factor in $treatments: + #set $factor_str = str($factor.name).encode('base64').replace('\n','') + + #for $level in $factor.rep_factorLevel: + #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value]) + #end for + + $factor_str + #end for + + #if $choose_blocking.choice == "true" + -b + #for blocking in $choose_blocking.blocking_repeat: + #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','') + + #for $block_iter in $blocking.block: + #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value]) + #set $blocking_str = $blocking_str+":"+$block_str + #end for + + $blocking_str + #end for + #end if + + -o $design_matrix + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + edgeR: Design- from Expression matrix ##################################### @@ -131,27 +135,8 @@ The test data is coming from: doi: 10.1093/bioinformatics/btt688. http://www.ncbi.nlm.nih.gov/pubmed/24319002 -Contact -------- - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.dtls.nl/ - -http://toolshed.g2.bx.psu.edu - -http://testtoolshed.g2.bx.psu.edu/ - - - - 10.1093/bioinformatics/btp616 - 10.1093/bioinformatics/btt688 - +@CONTACT@ + + + diff -r 049d8bc2214e -r a02794bb9073 edgeR_Differential_Gene_Expression.xml --- a/edgeR_Differential_Gene_Expression.xml Tue Sep 01 04:32:16 2015 -0400 +++ b/edgeR_Differential_Gene_Expression.xml Tue Sep 01 04:45:24 2015 -0400 @@ -2,28 +2,32 @@ RNA-Seq gene expression analysis using edgeR (R package) + + edgeR_macros.xml + + edger + source="both" + level="fatal" + description="Have the design- and expression-matrix been swapped?" /> + source="both" + level="fatal" /> + source="stderr" + level="log" /> + source="stderr" + level="log" /> + source="stderr" + level="warning" + description="LOCALE has not been set correctly" /> 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: ") @@ -594,9 +598,8 @@ This tool requires no specific configurations. The following dependencies are installed automatically: - R -- Bioconductor - - limma - - edgeR +- limma +- edgeR License ------- @@ -629,29 +632,8 @@ - http://www.ncbi.nlm.nih.gov/pubmed/24319002 - http://dx.doi.org/10.1093/bioinformatics/btt688 -Contact -------- - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.dtls.nl/ - -http://toolshed.g2.bx.psu.edu - -http://testtoolshed.g2.bx.psu.edu/ - -I would like to thank Hina Riaz - Naz Khan for her helpful contribution. +@CONTACT@ - - 10.1093/bioinformatics/btp616 - 10.1093/bioinformatics/btt688 - + diff -r 049d8bc2214e -r a02794bb9073 edgeR_macros.xml --- a/edgeR_macros.xml Tue Sep 01 04:32:16 2015 -0400 +++ b/edgeR_macros.xml Tue Sep 01 04:45:24 2015 -0400 @@ -0,0 +1,26 @@ + + Contact +------- + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands) on behalf of the Translational +Research IT (TraIT) project: + +http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch + +More tools by the Translational Research IT (TraIT) project can be found +in the following toolsheds: + +http://toolshed.g2.bx.psu.edu + +http://testtoolshed.g2.bx.psu.edu/ + +I would like to thank Hina Riaz - Naz Khan for her helpful contribution. + + + + 10.1093/bioinformatics/btp616 + 10.1093/bioinformatics/btt688 + + +