diff pangolin.xml @ 11:073de3fb84a0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 593540812c77e419c093a423e3598270a49b5e45"

--- a/pangolin.xml	Fri Oct 01 14:21:05 2021 +0000
+++ b/pangolin.xml	Fri Oct 22 10:12:25 2021 +0000
@@ -1,10 +1,14 @@
-<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
+<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
         <token name="@TOOL_VERSION@">3.1.14</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
+	<!-- the scorpio requirement is because pangolin got an update to use scorpio 0.3.13 (to detect AY.4.2 better) 
+             while still using the pangolin 3.1.14 code. when pangolin gets updated past 3.1.14 this requirement can
+             be removed -->
+	<requirement type="package" version="0.3.13">scorpio</requirement>
         <requirement type="package" version="0.23.0">csvtk</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
@@ -129,33 +133,6 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- testing with builtin data is too large -->
-        <!-- <test expect_num_outputs="1">
-            <param name="input1" value="test1.fasta"/>
-            <conditional name="db">
-                <param name="source" value="builtin" />
-            </conditional>
-            <output name="output1" ftype="tabular">
-                <assert_contents>
-                    <has_text text="Consensus_EB232-crude-prep_S297" />
-                    <has_n_lines n="1" />
-                </assert_contents>
-            </output>
-        </test> 
-        <test expect_num_outputs="1">
-            <param name="input1" value="multiple_alignment.fasta.gz"/>
-            <conditional name="db">
-                <param name="source" value="builtin" />
-            </conditional>
-            <output name="output1" ftype="tabular">
-                <assert_contents>
-                    <has_text text="Serbia" />
-                    <has_text text="Poland" />
-                    <has_text text="USA" />
-                    <has_n_lines n="34" />
-                </assert_contents>
-            </output>
-        </test> -->
         <!-- test include-header option -->
         <test expect_num_outputs="1">
             <param name="input1" value="multiple_alignment.fasta.gz"/>