changeset 4:cd5d77d118f2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06

--- a/freyja_boot.xml	Fri Nov 15 16:44:31 2024 +0000
+++ b/freyja_boot.xml	Wed Feb 19 11:08:52 2025 +0000
@@ -12,6 +12,7 @@
     <command detect_errors="exit_code"><![CDATA[
 @RUN_FREYJA_UPDATE_COMMAND@
 @PREPROCESS_VCF_INPUT@
+@CUSTOM_BARCODES_LINKING@
 freyja boot
     @STANDARD_INPUT_FOR_BOOT@
     --nt \${GALAXY_SLOTS:-4}
@@ -101,7 +102,40 @@
                 </assert_contents>
             </output>
         </test>
-    </tests>
+
+        <!-- Test 03: Test Custom Usher Barcode file -->
+        <test expect_num_outputs="4">
+            <conditional name="usher_update_option">
+                <param name="choice" value="custom"/>
+                <param name="usher_barcodes" location="https://zenodo.org/records/14888005/files/usher_barcodes.csv"/>
+            </conditional>
+            <param name="variants_file" value="variants.tsv"/>
+            <param name="depth_file" value="depths.tsv"/>
+            <param name="confirmedonly" value="false"/>
+            <param name="nb" value="10"/>
+            <param name="boxplot_pdf" value="true"/>
+            <output name="boot_lineages" ftype="csv">
+                <assert_contents>
+                    <has_text text="B.1.617.2"/>
+                </assert_contents>
+            </output>
+            <output name="boot_summarized" ftype="csv">
+                <assert_contents>
+                    <has_text text="Del"/>
+                </assert_contents>
+            </output>
+            <output name="boot_lineages_plot" ftype="pdf">
+                <assert_contents>
+                    <has_text text="Matplot"/>
+                </assert_contents>
+            </output>
+            <output name="boot_summarized_plot" ftype="pdf">
+                <assert_contents>
+                    <has_text text="Matplot"/>
+                </assert_contents>
+            </output>
+        </test>
+</tests>
     <help><![CDATA[
 @HELP_HEADER@
 

--- a/macros.xml	Fri Nov 15 16:44:31 2024 +0000
+++ b/macros.xml	Wed Feb 19 11:08:52 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.5.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
         <xrefs>
@@ -22,6 +22,16 @@
     freyja update &&
 #end if
 ]]></token>
+    <token name="@CUSTOM_BARCODES_LINKING@"><![CDATA[
+#if $usher_update_option.choice == 'custom'
+    ln -s '${usher_update_option.usher_barcodes}' usher_barcodes.csv &&
+#end if
+    ]]></token>
+    <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
+#if $usher_update_option.choice == 'custom'
+    --barcodes usher_barcodes.csv
+#end if
+]]></token>
     <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
 ln -s '$variants_file' 'variants_file.vcf' &&
 ]]></token>
@@ -41,11 +51,6 @@
 $confirmedonly
 --pathogen '$pathogen'
 ]]></token>
-    <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
-#if $usher_update_option.choice == 'custom'
-    --barcodes '${usher_update_option.usher_barcodes}'
-#end if
-]]></token>
     <token name="@DASH_COMMAND@"><![CDATA[
 echo '${plot_format.plot_title}' > plot_title.txt &&
 echo '${plot_format.plot_intro}' > plot_intro.txt &&