--- a/nanocompore_db.xml	Mon Jun 08 18:33:20 2020 +0000
+++ b/nanocompore_db.xml	Wed Jun 17 17:27:33 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
+<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy1">
     <description>Process SampComp results database</description>
     <macros>
         <import>macros.xml</import>
@@ -7,30 +7,55 @@
     <command detect_errors="exit_code"><![CDATA[
 mkdir results && 
 tar -xf $db --strip-components 1 -C results/ && 
- python '$__tool_directory__/NanocomporeDB_process.py'
- --db-path 'results/out_SampComp.db'
- --ref-fasta '$reference'
+python '$__tool_directory__/NanocomporeDB_process.py'
+--db-path 'results/out_SampComp.db'
+--ref-fasta '$reference'
 --annotation-bed '$annotation'
+$bedgraph
     ]]></command>
     <inputs>
         <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/>
         <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/>
         <param name="db" type="data" format="tar" label="SampComp Database" />
+        <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BEDGRAPH format instead of BED"/>
     </inputs>
     <outputs>
-        <data name="GMM_logit" format="bedgraph" from_work_dir="GMM_logit_pvalue.bedgraph" />
-        <data name="KS_dwell" format="bedgraph" from_work_dir="KS_dwell_pvalue.bedgraph" />
-        <data name="KS_intensity" format="bedgraph" from_work_dir="KS_intensity_pvalue.bedgraph" />
+        <data name="GMM_logit" format="bed" from_work_dir="GMM_logit_pvalue.bedgraph" label="${tool.name} on ${on_string}: GMM_logit">
+            <change_format>
+                <when input="bedgraph" value="true" format="bedgraph"/>
+            </change_format>
+        </data>
+
+        <data name="KS_dwell" format="bed" from_work_dir="KS_dwell_pvalue.bedgraph" label="${tool.name} on ${on_string}: KS_dwell">
+            <change_format>
+                <when input="bedgraph" value="true" format="bedgraph"/>
+            </change_format>
+        </data>
+
+        <data name="KS_intensity" format="bed" from_work_dir="KS_intensity_pvalue.bedgraph" label="${tool.name} on ${on_string}: KS_intensity">
+            <change_format>
+                <when input="bedgraph" value="true" format="bedgraph"/>
+            </change_format>
+        </data>
     </outputs>
     <tests>
         <test>
             <param name="reference" value="reference.fa"/>
             <param name="annotation" value="annot.bed"/>
             <param name="db" value="DB.tar"/>
+            <output name="GMM_logit" file="GMM_logit_pvalue.bed"/>
+            <output name="KS_dwell" file="KS_dwell_pvalue.bed"/>
+            <output name="KS_intensity" file="KS_intensity_pvalue.bed"/>
+        </test>
+        <test>
+            <param name="reference" value="reference.fa"/>
+            <param name="annotation" value="annot.bed"/>
+            <param name="db" value="DB.tar"/>
+            <param name="bedgraph" value="true"/>   
             <output name="GMM_logit" file="GMM_logit_pvalue.bedgraph"/>
             <output name="KS_dwell" file="KS_dwell_pvalue.bedgraph"/>
             <output name="KS_intensity" file="KS_intensity_pvalue.bedgraph"/>
-        </test>
+        </test>        
     </tests>
     <help><![CDATA[
 Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API.