--- a/edger.xml	Sun May 06 13:38:22 2018 -0400
+++ b/edger.xml	Sat Jan 05 05:32:02 2019 -0500
@@ -1,16 +1,16 @@
-<tool id="edger" name="edgeR" version="3.20.7.2">
+<tool id="edger" name="edgeR" version="3.22.5">
     <description>
         Perform differential expression of count data
     </description>
 
     <requirements>
-        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
-        <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
-        <requirement type="package" version="0.2.15">r-rjson</requirement>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="3.22.5">bioconductor-edger</requirement>
+        <requirement type="package" version="3.36.5">bioconductor-limma</requirement>
+        <requirement type="package" version="0.2.20">r-rjson</requirement>
+        <requirement type="package" version="1.20.2">r-getopt</requirement>
         <requirement type="package" version="1.4.30">r-statmod</requirement>
         <!-- required for alpha function used with plotMD -->
-        <requirement type="package" version="0.5.0">r-scales</requirement>
+        <requirement type="package" version="1.0.0">r-scales</requirement>
     </requirements>
 
     <version_command><![CDATA[
@@ -351,7 +351,11 @@
                     <has_text text="RData" />
                 </assert_contents>
             </output>
-            <output name="rscript" value="out_rscript.txt"/>
+            <output name="rscript">
+                <assert_contents>
+                    <has_text_matching expression="Task run time" />
+                </assert_contents>
+            </output>
         </test>
         <!-- Ensure secondary factors work -->
         <test>
@@ -378,7 +382,7 @@
                </element>
             </output_collection>
         </test>
-        <!-- Ensure factors file input works -->
+        <!-- Ensure factors file with unordered samples works -->
         <test>
             <param name="format" value="matrix" />
             <param name="ffile" value="yes" />
@@ -659,26 +663,6 @@
     11305      2528    2438    2493    1762     1942     2027
     ========== ======= ======= ======= ======== ======== ========
 
-**Factor Information:**
-Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
-
-Example:
-
-    ========== ============ =========
-    **Sample** **Genotype** **Batch**
-    ---------- ------------ ---------
-    WT1        WT           b1
-    WT2        WT           b2
-    WT3        WT           b3
-    Mut1       Mut          b1
-    Mut2       Mut          b2
-    Mut3       Mut          b3
-    ========== ============ =========
-
-*Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model.
-
-*Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
-
 
 **Gene Annotations:**
 Optional input for gene annotations, this can contain more
@@ -698,6 +682,27 @@
     11305        Abca2       ATP-binding cassette, sub-family A (ABC1), member 2
     ==========  ==========  ===================================================
 
+**Factor Information:**
+Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
+
+Example:
+
+    ========== ============ =========
+    **Sample** **Genotype** **Batch**
+    ---------- ------------ ---------
+    WT1        WT           b1
+    WT2        WT           b2
+    WT3        WT           b3
+    Mut1       Mut          b1
+    Mut2       Mut          b2
+    Mut3       Mut          b3
+    ========== ============ =========
+
+*Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used.
+
+*Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
+
+
 **Contrasts of Interest:**
 The contrasts you wish to make between levels.
 A common contrast would be a simple difference between two levels: "Mut-WT"