Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 115:f06dceb5b966 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty
| author | yhoogstrate |
|---|---|
| date | Tue, 01 Sep 2015 08:01:02 -0400 |
| parents | 5d7efbca6c75 |
| children | ed809072dc95 |
| files | edgeR_Concatenate_Expression_Matrices.xml edgeR_Convert_DGE_Table_to_Bedgraph.xml edgeR_Differential_Gene_Expression.xml |
| diffstat | 3 files changed, 5 insertions(+), 10 deletions(-) [+] |
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--- a/edgeR_Concatenate_Expression_Matrices.xml Tue Sep 01 07:54:09 2015 -0400 +++ b/edgeR_Concatenate_Expression_Matrices.xml Tue Sep 01 08:01:02 2015 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0"> +<tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0.b"> <description>Create a full expression matrix by selecting the desired columns from specific count tables</description> <macros>
--- a/edgeR_Convert_DGE_Table_to_Bedgraph.xml Tue Sep 01 07:54:09 2015 -0400 +++ b/edgeR_Convert_DGE_Table_to_Bedgraph.xml Tue Sep 01 08:01:02 2015 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> - <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0"> + <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0.b"> <description>EdgeR's "differentially expressed genes" table to bedgraph(s)</description> <macros>
--- a/edgeR_Differential_Gene_Expression.xml Tue Sep 01 07:54:09 2015 -0400 +++ b/edgeR_Differential_Gene_Expression.xml Tue Sep 01 08:01:02 2015 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a"> +<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.b"> <description>RNA-Seq gene expression analysis using edgeR (R package)</description> <macros> @@ -101,9 +101,6 @@ $output_format_images ' - #if $output_R: - > $output_R - #end if </command> <configfiles> @@ -238,7 +235,7 @@ diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x)) diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y)) 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") - mds_distance_logFC(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20) + points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20) text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) rm(diff_x,diff_y) @@ -270,7 +267,7 @@ diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x)) diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y)) 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") - mds_distance_BCV(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20) + points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20) text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) rm(diff_x,diff_y) @@ -432,8 +429,6 @@ <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option> <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option> <option value="make_output_heatmap_plot">Heatmap</option> - - <option value="make_output_R_stdout">R stdout</option> <option value="make_output_RData_obj">R Data object</option> </param>