# HG changeset patch
# User yhoogstrate
# Date 1441107398 14400
# Node ID f1ec1b5e9fa42e54f3656251408a7bf69916aed4
# Parent  b9abc9d3b42924e1974e96665b056a81ce23434b
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty

diff -r b9abc9d3b429 -r f1ec1b5e9fa4 edgeR_Design_from_Expression_Matrix.xml
--- a/edgeR_Design_from_Expression_Matrix.xml	Tue Sep 01 07:27:00 2015 -0400
+++ b/edgeR_Design_from_Expression_Matrix.xml	Tue Sep 01 07:36:38 2015 -0400
@@ -123,17 +123,11 @@
 Overview
 --------
 
-Create a design matrix by selecting the desired patients from an
-expression matrix.
+Create a design matrix by selecting the desired patients from an expression matrix.
 
 Input
 -----
 
-**References**
-
-The test data is coming from:  doi: 10.1093/bioinformatics/btt688.
-http://www.ncbi.nlm.nih.gov/pubmed/24319002
-
 @CONTACT@
     </help>
     
diff -r b9abc9d3b429 -r f1ec1b5e9fa4 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 01 07:27:00 2015 -0400
+++ b/tool_dependencies.xml	Tue Sep 01 07:36:38 2015 -0400
@@ -7,13 +7,12 @@
     <package name="design_matrix_creator" version="1.0.0">
         <install version="1.0">
             <actions>
-                <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/design_matrix_creator $INSTALL_DIR/bin/</action>
+                <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/design_matrix_creator $INSTALL_DIR/bin/design_matrix_creator</action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
                 </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
@@ -22,13 +21,12 @@
     <package name="edger_dge_table_to_bedgraph" version="1.0.0">
         <install version="1.0">
             <actions>
-                <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action>
+                <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/edger_dge_table_to_bedgraph</action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file>
                 </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>