# HG changeset patch
# User iuc
# Date 1750664131 0
# Node ID 7021ed347f7e0328ae4d6a2b86c1dd20bfed01e9
# Parent  93cfe7df7f8abf45162805ab31de95496c44a62d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 03d00ec10ba919fd8bac8d28f9b2b1e170fb3f55

diff -r 93cfe7df7f8a -r 7021ed347f7e artic_minion.xml
--- a/artic_minion.xml	Mon Feb 24 13:54:40 2025 +0000
+++ b/artic_minion.xml	Mon Jun 23 07:35:31 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy1" profile="23.2">
+<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy0" profile="23.2">
     <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
     <macros>
         <import>macros.xml</import>
@@ -59,6 +59,8 @@
             --min-mapq $min_mapq
             --primer-match-threshold $primer_match_threshold
             $align_consensus
+            $linearise_fasta
+            $allow_mismatched_primers
 
         #if $normalise > 0:
             --normalise ${normalise}
@@ -97,6 +99,14 @@
         label="Align Consensus to reference"
         help="Run a MAFFT to align consensus to reference" />
 
+        <param argument="--linearise-fasta" type="boolean" truevalue="--linearise-fasta" falsevalue=""
+        label="Linearise output fasta"
+        help="Output linearised (unwrapped) FASTA consensus files" />
+
+        <param argument="--allow-mismatched-primers" type="boolean" truevalue="--allow-mismatched-primers" falsevalue=""
+        label="Allow primer mismatch"
+        help="Reads will not be discarded by align_trim if they appear to have primers from different amplicons." />
+
         <!-- Primer and Reference fetching -->
         
         <conditional name="fetch_primer_scheme">
@@ -224,7 +234,7 @@
             </conditional>
             <output name="consensus_fasta">
                 <assert_contents>
-                    <has_line line=">test.fastq.gz/MN908947.3/ARTIC/clair3 MN908947.3" />
+                    <has_text text=">test.fastq.gz MN908947.3_artic-network/fieldbioinformatics_" />
                 </assert_contents>
             </output>
             <output name="alignment_trimmed">
@@ -234,7 +244,7 @@
             </output>
             <output name="variants_merged_vcf">
                 <assert_contents>
-                    <has_size value="900" delta="200" />
+                    <has_size value="1800" delta="200" />
                 </assert_contents>
             </output>
         </test>
@@ -258,7 +268,7 @@
             </conditional>
             <output name="consensus_fasta">
                 <assert_contents>
-                    <has_line line=">test.fastq.gz/MN908947.3/ARTIC/clair3 MN908947.3" />
+                    <has_text text=">test.fastq.gz MN908947.3_artic-network/fieldbioinformatics_" />
                 </assert_contents>
             </output>
             <output name="alignment_trimmed">
@@ -268,7 +278,7 @@
             </output>
             <output name="variants_merged_vcf">
                 <assert_contents>
-                    <has_size value="3200" delta="200" />
+                    <has_size value="1800" delta="200" />
                 </assert_contents>
             </output>
         </test>
@@ -295,7 +305,7 @@
             </conditional>
             <output name="consensus_fasta">
                 <assert_contents>
-                    <has_line line=">test.fastq.gz/MN908947.3/ARTIC/clair3 MN908947.3" />
+                    <has_text text=">test.fastq.gz MN908947.3_artic-network/fieldbioinformatics_" />
                 </assert_contents>
             </output>
             <output name="alignment_trimmed">
@@ -305,7 +315,7 @@
             </output>
             <output name="variants_merged_vcf">
                 <assert_contents>
-                    <has_size value="3200" delta="200" />
+                    <has_size value="1800" delta="200" />
                 </assert_contents>
             </output>
         </test>
diff -r 93cfe7df7f8a -r 7021ed347f7e macros.xml
--- a/macros.xml	Mon Feb 24 13:54:40 2025 +0000
+++ b/macros.xml	Mon Jun 23 07:35:31 2025 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.6.0</token>
+    <token name="@TOOL_VERSION@">1.7.3</token>
     <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
     
     <xml name="requirements">