diff ivar_removereads.xml @ 12:8c05afb547fa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
author iuc
date Mon, 13 Feb 2023 17:31:02 +0000
parents 7f1cfa4c0e32
children
line wrap: on
line diff
--- a/ivar_removereads.xml	Wed Jan 11 09:56:04 2023 +0000
+++ b/ivar_removereads.xml	Mon Feb 13 17:31:02 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
+<tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Remove reads from trimmed BAM file</description>
     <macros>
         <import>macros.xml</import>
@@ -60,9 +60,14 @@
                 <param name="computed" value="no"/>
                 <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
             </conditional>
+            <assert_stdout>
+                <!-- check that primer pairs are picked up correctly
+                from the amplicon info file -->
+                <has_text text="400_18_out_L**&#009;400_18_out_R**&#009;400_23_out_L&#009;400_23_out_R&#009;400_32_out_L&#009;400_32_out_R"/>
+            </assert_stdout>
             <output name="output_bam" ftype="bam">
                 <assert_contents>
-                    <has_size value="3185672" delta="1000"/>
+                    <has_size value="3130923" delta="1000"/>
                 </assert_contents>
             </output>
         </test>
@@ -73,9 +78,14 @@
             <conditional name="amplicons">
                 <param name="computed" value="yes"/>
             </conditional>
+            <assert_stdout>
+                <!-- check that primer pairs are picked up correctly
+                from the autogenerated amplicon info file -->
+                <has_text text="400_18_out_L**&#009;400_18_out_R**&#009;400_23_out_L&#009;400_23_out_R&#009;400_32_out_L&#009;400_32_out_R"/>
+            </assert_stdout>
             <output name="output_bam" ftype="bam">
                 <assert_contents>
-                    <has_size value="3185672" delta="1000"/>
+                    <has_size value="3130923" delta="1000"/>
                 </assert_contents>
             </output>
         </test>