--- a/abims_sartools_edger.xml	Mon Oct 01 05:07:56 2018 -0400
+++ b/abims_sartools_edger.xml	Thu Jan 07 11:12:01 2021 +0000
@@ -1,84 +1,68 @@
-<tool id="sartools_edger" name="SARTools edgeR" version="@WRAPPER_VERSION@.0">
+<tool id="sartools_edger" name="SARTools edgeR" version="@TOOL_VERSION@+galaxy0">
     
-    <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description>Compare two or more biological conditions in a RNA-Seq framework with edgeR</description>
     
     <macros>
-    	<import>macros.xml</import>
+        <import>macros.xml</import>
     </macros>
     
     <expand macro="requirements"/>
     <expand macro="stdio"/>
 
     
-    <!-- [REQUIRED] The command to execute -->
-    <command interpreter="python"><![CDATA[
-	
-	abims_sartools_edger_wrapper.py
-	## parameters
-	@COMMAND_BASIC_PARAMETERS@
-    	#if str( $advanced_parameters.adv_param ) == "show":
-            @COMMAND_BATCH_PARAM@
-	    --alpha $advanced_parameters.alpha
-	    --pAdjustMethod $advanced_parameters.pAdjustMethod
-	    --cpmCutoff $advanced_parameters.cpmCutoff
-	    --geneSelection $advanced_parameters.geneSelection
-	    --normalizationMethod $advanced_parameters.normalizationMethod
-	    --colors $advanced_parameters.colors
-            --forceCairoGraph $advanced_parameters.forceCairoGraph
-    	#end if
-	## ouputs
-	@COMMAND_OUTPUTS@
+    <command><![CDATA[
+ 
+python '$__tool_directory__/abims_sartools_edger_wrapper.py'
+## parameters
+@COMMAND_BASIC_PARAMETERS@
+@COMMAND_BATCH_PARAM@
+--alpha '$advanced_parameters.alpha'
+--pAdjustMethod '$advanced_parameters.pAdjustMethod'
+--cpmCutoff '$advanced_parameters.cpmCutoff'
+--geneSelection '$advanced_parameters.geneSelection'
+--normalizationMethod '$advanced_parameters.normalizationMethod'
+--colors "'$advanced_parameters.colors'"
+--forceCairoGraph '$advanced_parameters.forceCairoGraph'
+## ouputs
+@COMMAND_OUTPUTS@
         
     ]]></command>
     
-    <!-- [REQUIRED] Input files and tool parameters -->
     <inputs>
         
         <expand macro="basic_parameters" />
  
-        <conditional name="advanced_parameters" >
-            <param name="adv_param" type="select" label="Advanced Parameters" help="" >
-                <option value="hide" selected="true">Hide</option>
-                <option value="show">Show</option>
+        <section name="advanced_parameters" title="Advanced Parameters" expanded="false" >
+            <expand macro="batch_param" />
+            <expand macro="alpha_param" />
+            <expand macro="padjustmethod_param" />
+            <param type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" argument="--cpmCutoff" help="Set to 0 to disable filtering. Default is 1." />
+            <param name="geneSelection" type="select" label="Selection of the features in MDSPlot" argument="--gene.selection" help="Default is 'pairwise'." >
+                <option value="pairwise" selected="true">pairwise</option>
+                <option value="common">common</option>
             </param>
-            <when value="hide" />
-            <when value="show">
-		<expand macro="batch_param" />
-		<expand macro="alpha_param" />
-		<expand macro="padjustmethod_param" />
-		<param type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" argument="--cpmCutoff" help="Set to 0 to disable filtering. Default is 1." />
-		<param name="geneSelection" type="select" label="Selection of the features in MDSPlot" argument="--gene.selection" help="Default is 'pairwise'." >
-                	<option value="pairwise" selected="true">pairwise</option>
-                	<option value="common">common</option>
-		</param>
-		<param type="select" label="Normalization method in calcNormFactors" argument="--normalizationMethod" help="'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
-                	<option value="TMM" selected="true">TMM</option>
-                	<option value="RLE">RLE</option>
-                	<option value="upperquartile">upperquartile</option>
-		</param>
-		<expand macro="colors_param" />
-		<expand macro="forceCairoGraph_param" />
-            </when>
-        </conditional>
+            <param type="select" label="Normalization method in calcNormFactors" argument="--normalizationMethod" help="'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
+                <option value="TMM" selected="true">TMM</option>
+                <option value="RLE">RLE</option>
+                <option value="upperquartile">upperquartile</option>
+            </param>
+            <expand macro="colors_param" />
+            <expand macro="forceCairoGraph_param" />
+        </section>
 
     </inputs>
     
-    <!-- [REQUIRED] Output files -->
     <outputs>
         
         <expand macro="outputs" /> 
               
     </outputs>
     
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
     <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
         <test>
-	    <!-- Test with 2 conditions, 2 replicates, 10 features -->
+     <!-- Test with 2 conditions, 2 replicates, 10 features -->
             <param name="targetFile" dbkey="?" value="target_small.txt" />
             <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/>
-	        <param name="adv_param" value="show"/>
             <output name="log">
                 <assert_contents>
                     <has_text text="KO vs WT    5      4    9" />
@@ -86,24 +70,22 @@
                 </assert_contents>
             </output>
         </test>
-<!--        <test>
+<!--    <test>
 -->        <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect -->
-<!--            <param name="targetFile" dbkey="?" value="targetT048_small.txt" />
+<!--        <param name="targetFile" dbkey="?" value="targetT048_small.txt" />
             <param name="rawDir"   value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/>
-	    <param name="condRef" value="T0"/>
-	    <param name="adv_param" value="show"/>
-	    <param name="condition" value="true"/>
+            <param name="condRef" value="T0"/>
+            <param name="condition" value="true"/>
             <output name="tables_html" file="SARTools_edgeR_targetT048_small_tables.html" lines_diff="12">
-            	<extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/>
-            	<extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/>
-            	<extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/>
-	    </output>
+                <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/>
+                <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/>
+                <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/>
+            </output>
         </test>
--->        <test>
+-->     <test>
         <!-- Test with 2 conditions, 2 replicates, 8217 features -->
             <param name="targetFile" dbkey="?" value="target.txt" />
             <param name="rawDir"   value="raw.zip" dbkey="?" ftype="zip"/>
-	        <param name="adv_param" value="show"/>
             <output name="log">
                 <assert_contents>
                     <has_text text="KO vs WT    2691   2713 5404" />
@@ -111,22 +93,20 @@
                 </assert_contents>
             </output>
         </test>
-<!--        <test>
+<!--    <test>
 -->        <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->
-<!--            <param name="targetFile" dbkey="?" value="targetT048.txt" />
+<!--        <param name="targetFile" dbkey="?" value="targetT048.txt" />
             <param name="rawDir"   value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>
-	    <param name="condRef" value="T0"/>
-	    <param name="adv_param" value="show"/>
-	    <param name="condition" value="true"/>
+            <param name="condRef" value="T0"/>
+            <param name="condition" value="true"/>
             <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14">
-            	<extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/>
-            	<extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/>
-            	<extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/>
-	    </output>
+                <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/>
+                <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/>
+                <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/>
+            </output>
         </test>
--->    </tests>
+--> </tests>
     
-    <!-- [OPTIONAL] Help displayed in Galaxy -->
     <help><![CDATA[
 
 @HELP_AUTHORS@
@@ -153,15 +133,15 @@
 Parameters
 ----------
 
-	@HELP_BASIC_PARAMETERS@
-	* **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account);
-	* **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
-	* **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods);
-	* **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering);
-	* **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common);
-	* **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile";
-	* **colors:** colors used for the figures (one per biological condition), 8 are given by default.
-	* **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
+ @HELP_BASIC_PARAMETERS@
+ * **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account);
+ * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
+ * **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods);
+ * **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering);
+ * **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common);
+ * **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile";
+ * **colors:** colors used for the figures (one per biological condition), 8 are given by default.
+ * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
 
 
 ------------
@@ -170,7 +150,7 @@
 
 @HELP_OUTPUT_FILES@
 
-		
+  
 ---------------------------------------------------
 
 [1] G.-K. Smyth. Limma: linear models for microarray data. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer, New York, 2005.
@@ -184,7 +164,7 @@
 [5] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001.
 
 
-   ]]></help>
+    ]]></help>
 
    <citations>
         <expand macro="common_citations" />