diff pangolin.xml @ 4:42126b414951 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"

--- a/pangolin.xml	Wed May 19 13:32:34 2021 +0000
+++ b/pangolin.xml	Thu Jun 03 06:38:26 2021 +0000
@@ -1,7 +1,7 @@
-<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.3.8</token>
+        <token name="@TOOL_VERSION@">3.0.3</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
@@ -18,6 +18,7 @@
         #if str($db.source) == "download" or str($db.source) == "builtin"
             --datadir 'datadir'
         #end if
+        $usher
         $alignment
         --outfile report.csv 
         --max-ambig $max_ambig
@@ -34,7 +35,8 @@
     ]]></command>
     <inputs>
         <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> 
-        <param name="alignment" type="boolean" label="Generate output alignment" 
+        <param argument="--usher" type="boolean" label="Use UShER model" truevalue="--usher" falsevalue="" help="Use UShER model instead of default pangoLEARN model" />
+        <param argument="--alignment" type="boolean" label="Generate output alignment" 
             truevalue="--alignment" falsevalue="" /> 
         <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 
             value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
@@ -56,7 +58,8 @@
                         <column name="value" index="0" />
                         <column name="name" index="1" />
                         <column name="path" index="3" />
-                        <filter type="sort_by" column="0"/>
+                        <filter type="sort_by" column="0" />
+                        <filter type="static_value" column="2" value="3.0" />
                     </options>
                 </param>
             </when>
@@ -67,7 +70,7 @@
     <outputs>
         <data name="output1" format="tabular" label="pangolin on ${on_string}">
             <actions>
-                <action name="column_names" type="metadata" default="taxon,lineage,probability,pangoLEARN_version,status,note" />
+                <action name="column_names" type="metadata" default="taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,version,pangolin_version,pangoLEARN_version,pango_version,status,note" />
             </actions>
         </data>
         <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
@@ -82,7 +85,22 @@
             </conditional>
             <output name="output1" ftype="tabular">
                 <assert_contents>
-                    <has_text text="B.1.1" />
+                    <has_text_matching expression="B.1.1\t0.0" />
+                    <has_text text="passed_qc" />
+                    <has_n_lines n="1" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test UShER mode -->
+        <test expect_num_outputs="1">
+            <param name="input1" value="test1.fasta"/>
+            <param name="usher" value="true" />
+            <conditional name="db">
+                <param name="source" value="download" />
+            </conditional>
+            <output name="output1" ftype="tabular">
+                <assert_contents>
+                    <has_text_matching expression="B.1.1.409\t\t*PUSHER" />
                     <has_text text="passed_qc" />
                     <has_n_lines n="1" />
                 </assert_contents>
@@ -96,7 +114,7 @@
             </conditional>
             <output name="output1" ftype="tabular">
                 <assert_contents>
-                    <has_text text="B.1.1" />
+                    <has_text_matching expression="B.1.1\t0.0" />
                     <has_text text="passed_qc" />
                     <has_n_lines n="1" />
                 </assert_contents>
@@ -108,7 +126,8 @@
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="1">
+        <!-- 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" />
@@ -119,7 +138,7 @@
                     <has_n_lines n="1" />
                 </assert_contents>
             </output>
-        </test>
+        </test> 
         <test expect_num_outputs="1">
             <param name="input1" value="multiple_alignment.fasta.gz"/>
             <conditional name="db">
@@ -133,13 +152,13 @@
                     <has_n_lines n="34" />
                 </assert_contents>
             </output>
-        </test>
+        </test> -->
         <!-- test include-header option -->
         <test expect_num_outputs="1">
             <param name="input1" value="multiple_alignment.fasta.gz"/>
             <param name="include_header" value="true" />
             <conditional name="db">
-                <param name="source" value="builtin" />
+                <param name="source" value="download" />
             </conditional>
             <output name="output1" ftype="tabular">
                 <assert_contents>