# 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
-
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+ 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
+
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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
-
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- "c3" in columns
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- "c4" in columns
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- "c5" in columns
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- "c6" in columns
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- "c7" in columns
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- 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
+
+
+
+
+
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+
+ "c3" in columns
+
+
+
+ "c4" in columns
+
+
+
+ "c5" in columns
+
+
+
+ "c6" in columns
+
+
+
+ "c7" in columns
+
+
+
+
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+
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+
+
+
+ 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
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+ 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
+
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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
+
+
+