diff edgeR_Differential_Gene_Expression.xml @ 108:a02794bb9073 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty

--- 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 @@
 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a">
     <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
     
+    <macros>
+        <import>edgeR_macros.xml</import>
+    </macros>
+    
     <requirements>
         <requirement type="package" version="3.11.0">edger</requirement>
     </requirements>
     
     <stdio>
         <regex match="Error in[^a-z]+contrasts"
-                source="both"
-                level="fatal"
-                description="Have the design- and expression-matrix been swapped?" />
+               source="both"
+               level="fatal"
+               description="Have the design- and expression-matrix been swapped?" />
         <regex match="Execution halted"
-                source="both"
-                level="fatal" />
+               source="both"
+               level="fatal" />
         <regex match="Calculating library sizes from column" 
-                source="stderr" 
-                level="log" />
+               source="stderr" 
+               level="log" />
         <regex match="During startup - Warning messages"
-                source="stderr"
-                level="log" />
+               source="stderr"
+               level="log" />
         <regex match="Setting LC_[^ ]+ failed"
-                source="stderr"
-                level="warning"
-                description="LOCALE has not been set correctly" />
+               source="stderr"
+               level="warning"
+               description="LOCALE has not been set correctly" />
     </stdio>
     
     <version_command>echo $(R --version | grep version | grep -v GNU) " , EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null | grep -v -i "WARNING: ")</version_command>
@@ -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@
     </help>
     
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/btp616</citation>
-        <citation type="doi">10.1093/bioinformatics/btt688</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>