--- a/run_de_analysis.xml	Sun Dec 19 16:04:45 2021 +0000
+++ b/run_de_analysis.xml	Tue Apr 11 19:41:06 2023 +0000
@@ -1,30 +1,21 @@
-<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@">
+<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>using a Trinity assembly</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-    <expand macro="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="1.18.1">bioconductor-deseq2</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
 
-        ln -f -s '${matrix}' "input.matrix"
-
+        ln -f -s '${matrix}' input.matrix
         &&
-
         run_DE_analysis.pl
-
-        --matrix "input.matrix"
-
-        --samples_file '${samples}'
-
+        --matrix input.matrix
+        --samples_file '${samples_file}'
         --method ${method_choice.method}
 
         #if $method_choice.method == "edgeR":
-            --dispersion ${method_choice.edger_dispersion}
+            --dispersion ${method_choice.dispersion}
         #end if
 
         #if $method_choice.method == "ROTS":
@@ -46,34 +37,32 @@
 
     ]]></command>
     <inputs>
-        <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of Build expression matrix - matrix of raw read counts (not normalized!)"/>
-        <param format="tabular" name="samples" argument="--samples_file" type="data" label="Sample description" help="file describing samples and replicates"/>
+        <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="output of Build expression matrix - matrix of raw read counts (not normalized!)"/>
+        <param argument="--samples_file" format="tabular" type="data" label="Sample description" help="file describing samples and replicates"/>
 
         <conditional name="method_choice">
-            <param type="select" name="method" argument="--method" label="Differential analysis method">
+            <param type="select" argument="--method" label="Differential analysis method">
                 <option value="edgeR">edgeR</option>
                 <option value="DESeq2">DESeq2</option>
                 <option value="voom">voom</option>
                 <option value="ROTS">ROTS</option>
             </param>
             <when value="edgeR">
-                <param name="edger_dispersion" argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
+                <param argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
             </when>
             <when value="ROTS">
-                <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="number of bootstraps and permutation resampling" />
-                <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="largest top genes size" />
+                <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="Number of bootstraps and permutation resampling" />
+                <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="Largest top genes size" />
             </when>
-            <when value="voom">
-            </when>
-            <when value="DESeq2">
-            </when>
+            <when value="voom"/>
+            <when value="DESeq2" />
         </conditional>
 
         <section name="additional_params" title="Additional Options" expanded="False">
             <param name="min_cpm" type="integer" value="1" label="Minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/>
             <param name="min_reps" type="integer" value="2" label="Minimum number of replicates meeting minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/>
-            <param name="reference_sample" argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
-            <param format="tabular" name="contrasts" argument="--contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
+            <param argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
+            <param argument="--contrasts" optional="true" type="data" format="tabular" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
         </section>
     </inputs>
     <outputs>
@@ -90,7 +79,7 @@
     <tests>
         <test>
             <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
-            <param name="samples" value="count/samples.txt"/>
+            <param name="samples_file" value="count/samples.txt"/>
             <param name="method" value="DESeq2"/>
             <output_collection name="DE_results">
                 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
@@ -110,7 +99,7 @@
         </test>
         <test>
             <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
-            <param name="samples" value="count/samples.txt"/>
+            <param name="samples_file" value="count/samples.txt"/>
             <param name="method" value="edgeR"/>
             <output_collection name="DE_results">
                 <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results"/>
@@ -130,7 +119,7 @@
         </test>
         <test>
             <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
-            <param name="samples" value="count/samples.txt"/>
+            <param name="samples_file" value="count/samples.txt"/>
             <param name="method" value="voom"/>
             <output_collection name="DE_results">
                 <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results"/>