diff ivar_trim.xml @ 12:e3bb03cf207a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324

--- a/ivar_trim.xml	Wed Jul 13 15:18:33 2022 +0000
+++ b/ivar_trim.xml	Wed Jan 11 09:55:20 2023 +0000
@@ -1,13 +1,10 @@
-<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy4" profile="21.01">
+<tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
     <description>Trim reads in aligned BAM</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="3.8.1">python</requirement>
-        <requirement type="package" version="1.15">samtools</requirement>
-    </expand>
-    <expand macro="version_command" />
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         #if $primer.source == 'history'
             cp '$primer.input_bed' bed.bed &&
@@ -114,7 +111,18 @@
                 <param name="input_bed" value="zika/db/zika_primers.bed" />
             </conditional>
             <param name="input_bam" value="zika/Z52_b.sorted.bam" />
-            <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
+            <output name="output_bam" ftype="bam">
+                <assert_contents>
+                    <has_size value="4023965" delta="1000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="Found 68 primers in BED file"/>
+                <has_text text="Using Region: PRV"/>
+                <has_text text="Found 40964 mapped reads"/>
+                <has_text text="reads were quality trimmed below the minimum length of 30 bp and were not written to file"/>
+                <has_text text="reads that started outside of primer regions were not written to file"/>
+            </assert_stdout>
         </test>
         <test>
             <conditional name="primer">