diff limma_voom.xml @ 11:7e8af58c8052 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc

--- a/limma_voom.xml	Fri Jun 08 02:20:16 2018 -0400
+++ b/limma_voom.xml	Mon Jun 11 08:18:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="limma_voom" name="limma" version="3.34.9.6">
+<tool id="limma_voom" name="limma" version="3.34.9.7">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>
@@ -81,10 +81,15 @@
     -x
 #end if
 
+#if $out.libinfo:
+    -L
+#end if
+
 #if $out.rdaOption:
     -r
 #end if
 
+
 -l '$adv.lfc'
 -p '$adv.pVal'
 -d '$adv.pAdjust'
@@ -271,6 +276,10 @@
                 label="Output Normalised Counts Table?"
                 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
             </param>
+            <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                label="Output Library information file?"
+                help="Output a tabular file showing the library sizes, normalisation factors and effective library sizes for the samples. Default: No">
+            </param>
             <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
             <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
                 label="Output RData file?"
@@ -317,6 +326,9 @@
         <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
             <filter>out['rscript']</filter>
         </data>
+        <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information">
+            <filter>out['libinfo']</filter>
+        </data>
     </outputs>
 
     <tests>
@@ -796,6 +808,7 @@
 Optionally, under **Output Options** you can choose to output
 
     * a normalised counts table
+    * a library size information file
     * the R script used by this tool
     * an RData file