--- a/nanoplot.xml	Tue Oct 23 08:30:58 2018 -0400
+++ b/nanoplot.xml	Thu Jun 20 10:18:48 2019 -0400
@@ -1,8 +1,12 @@
-<tool id="nanoplot" name="NanoPlot" version="1.13.0">
+<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0">
     <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.25.0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.18.2">nanoplot</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
     </requirements>
+    <version_command>NanoPlot --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
 
@@ -350,7 +354,6 @@
                 optional="true"
                 label="Specify the output format of the plots.">
                 <option selected="True" value="png">png</option>
-                <option value="jpg">jpg</option>
                 <option value="svg">svg</option>
             </param>
             <param
@@ -385,13 +388,11 @@
         <data name="nanostats_post_filtering" format="txt" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
         <data name="read_length" format="png" from_work_dir="HistogramReadlength.*" label="${tool.name} on ${on_string}: Histogram Read Length ">
             <change_format>
-                <when input="customization.format" value="jpg" format="jpg"/>
                 <when input="customization.format" value="svg" format="svg"/>
             </change_format>
         </data>
         <data name="log_read_length" format="png" from_work_dir="LogTransformed_HistogramReadlength.*" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length ">
             <change_format>
-                <when input="customization.format" value="jpg" format="jpg"/>
                 <when input="customization.format" value="svg" format="svg"/>
             </change_format>
         </data>
@@ -408,12 +409,10 @@
             <section name="customization">
                 <param name="plots" value="hex,kde"/>
                 <param name="title" value="My Plot"/>
-                <param name="format" value="jpg"/>
             </section>
             <output name="output_html" file="NanoPlot-report.html" ftype="html"/>
-            <output name="nanostats" file="NanoStats.txt" ftype="txt"/>
             <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/>
-            <output name="read_length" file="HistogramReadlength.jpg" ftype="jpg" compare="sim_size" delta="30000"/>
+            <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/>
         </test>
         <test>
             <conditional name="reads">
@@ -429,14 +428,30 @@
                 <param name="format" value="svg"/>
                 <param name="noN50" value="True"/>
             </section>
-            <output name="output_html" file="bam-report.html" ftype="html" compare="sim_size" delta="50000"/>
+            <output name="output_html" file="bam-report.html" ftype="html">
+                <assert_contents>
+                    <has_text text="html"/>
+                    <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
+                </assert_contents>
+            </output>
             <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/>
         </test>
-
+        <test><!-- test with multiple input files -->
+            <conditional name="reads">
+                <param name="type" value="fasta"/>
+                <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />
+            </conditional>
+            <output name="output_html" ftype="html">
+                <assert_contents>
+                    <has_text text="html"/>
+                    <not_has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
+                    <has_text text="&lt;td&gt;9.0&lt;/td&gt;"/> <!--check both files used 4+5 reads -->
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
         <![CDATA[
-
         **What it does**
 
         NanoPlot_ is a plotting tool for long read sequencing data and alignments written by `Wouter De Coster`_