diff tracy_align.xml @ 1:b0afd480167a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8eb3532d394f6a44d1edbcbe5ef05fd0474cdab3

--- a/tracy_align.xml	Tue Oct 12 14:20:14 2021 +0000
+++ b/tracy_align.xml	Thu Mar 20 07:18:02 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="tracy_align" name="tracy Align" version="@TOOL_VERSION@+galaxy0" profile="20.09">
+<tool id="tracy_align" name="tracy Align" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>chromatogram to a FASTA reference</description>
     <macros>
         <import>macros.xml</import>
@@ -46,39 +46,38 @@
         <expand macro="tabular_output" toolname="align" />
     </outputs>
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="2"> <!-- test 1 -->
             <param name="reference" value="reference1.fasta" ftype="fasta" />
             <param name="index_genome" value="false" />
-            <param name="tracefile" value="input1.ab1" ftype="ab1" />
+            <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
             <output name="out_report" value="out1.txt" ftype="txt" />
             <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />    
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="2"> <!-- test 2 -->
             <param name="reference" value="reference1.fasta" ftype="fasta" />
             <param name="index_genome" value="true" />
-            <param name="tracefile" value="input1.ab1" ftype="ab1" />
+            <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
             <output name="out_report" value="out2.txt" ftype="txt" />
             <output name="out_alignment" value="out2.fasta" ftype="fasta" lines_diff="2" />    
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="4"> <!-- test 3 -->
             <param name="reference" value="reference1.fasta" ftype="fasta" />
             <param name="index_genome" value="false" />
-            <param name="tracefile" value="input1.ab1" ftype="ab1" />
+            <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
             <param name="optional_outputs" value="json,tabular" />
             <output name="out_report" value="out1.txt" ftype="txt" />
             <output name="out_json" ftype="json">
                 <assert_contents>
-                    <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
+                    <has_text text='"peakA": [20, 20, 20, 19, 19' />
                 </assert_contents>
             </output>
             <output name="out_stats" ftype="tabular">
-                <assert_contents>
-                    <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" />
+                <assert_contents> 
+                    <has_text_matching expression="8\s20\s4\s14\s37\s1\sT\sR\sN\s0\sY" />
                 </assert_contents>
             </output>
             <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />    
         </test>
-
     </tests>
     <help><![CDATA[
 **What it does**.