Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 122:7bb87a6bc4d5 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc
| author | yhoogstrate |
|---|---|
| date | Wed, 16 Dec 2015 11:15:18 -0500 |
| parents | 6c90a67a13fa |
| children | 4eb118759971 |
| files | edgeR_Differential_Gene_Expression.xml tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/edgeR_Differential_Gene_Expression.xml Mon Dec 14 05:10:49 2015 -0500 +++ b/edgeR_Differential_Gene_Expression.xml Wed Dec 16 11:15:18 2015 -0500 @@ -288,6 +288,11 @@ if(output_MDSplot_logFC != "/dev/null" || output_MDSplot_logFC_coordinates != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") { write("Calculating MDS plot (logFC method)",stdout()) n_dim <- nrow(dge\$samples) + + if(n_dim >= nrow(dge\$counts)) { + n_dim <- 3 + } + mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1)) dev.off()# Kill it
--- a/tool_dependencies.xml Mon Dec 14 05:10:49 2015 -0500 +++ b/tool_dependencies.xml Wed Dec 16 11:15:18 2015 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="edger" version="3.11.0"> - <repository changeset_revision="6ffda6224a37" name="package_r_edger_3_11_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="330f615d062e" name="package_r_edger_3_11_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="design_matrix_creator" version="1.0.0">