Merge pull request #6693 from ammaraziz/update-artic

Update artic to v.1.6.0
galaxyproject · Feb 21, 2025 · 20c6e31 · 20c6e31
2 parents c45c312 + ca8347e
commit 20c6e31
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Showing 24 changed files with 844 additions and 3,278 deletions.
diff --git a/tools/artic/artic_guppyplex.xml b/tools/artic/artic_guppyplex.xml
@@ -1,11 +1,9 @@
-<tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy2" profile="20.09">
+<tool id="artic_guppyplex" name="ARTIC guppyplex" version="@TOOL_VERSION@+galaxy0" profile="20.09">
     <description>Filter Nanopore reads by read length and (optionally) quality</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement>
-    </requirements>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
         mkdir inputs &&
@@ -23,7 +21,10 @@
         #else:
             #set $compressed = next(iter($input.reads)).is_of_type("fastq.gz", "fastqsanger.gz")
         #end if
-        artic guppyplex --min-length $min_length --max-length $max_length
+
+        artic guppyplex 
+            --min-length $min_length 
+            --max-length $max_length
         #if $min_quality == 0:
             --skip-quality-check
         #else:
@@ -67,11 +68,12 @@ ln -s '$elem' inputs/${i}.${elem.ext} &&
                 help="Multiple datasets selected here will get combined into a single output for a single assumed sample. Select a nested list to have its inner lists interpreted as data from one sample each and to obtain one output per inner list." />
             </when>
         </conditional>
-        <param name="max_length" type="integer" label="Remove reads longer than" value="700" help="remove reads greater than this number of base pairs" />
-        <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" />
-        <param name="min_quality" type="integer" min="0" value="7"
-        label="Eliminate reads with a mean base quality score of less than"
-        help="Set to 0 to skip the quality check." />
+        <param name="max_length" type="integer" value="700" min="1" label="Maximum read length" help="Remove reads greater than this number of base pairs" />
+        <param name="min_length" type="integer" value="400" min="1" label="Minimum read length" help="Remove reads less than this number of base pairs" />
+        <param name="min_quality"
+        optional="true" type="integer" min="0" value="7"
+        label="Minimum read quality"
+        help="Remove reads with average quality lower than this number. Set to 0 to skip the quality check." />
     </inputs>
     <outputs>
         <data name="output" format_source="reads" from_work_dir="guppyplex_out.fastq*" />
@@ -80,18 +82,24 @@ ln -s '$elem' inputs/${i}.${elem.ext} &&
         <test>
             <conditional name="input">
                 <param name="structure" value="one_to_one" />
-                <param name="reads" value="test.fastq" />
+                <param name="reads" value="test.fastq.gz" />
             </conditional>
-            <output name="output" file="gupplyplex_output.fastq"/>
+            <output name="output">
+                <assert_contents>
+                    <has_size value="72300" delta="1000" />
+                </assert_contents>
+            </output>
         </test>
         <test>
             <conditional name="input">
                 <param name="structure" value="one_to_many" />
-                <param name="reads" value="test.fastq,test.fastq" />
+                <param name="reads" value="test.fastq.gz,test.fastq.gz" />
             </conditional>
-            <!-- guppyplex drops duplicate reads so we don't need a new
-            test file for checking this branch -->
-            <output name="output" file="gupplyplex_output.fastq"/>
+            <output name="output">
+                <assert_contents>
+                    <has_size value="72300" delta="200" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/artic/artic_minion.xml b/tools/artic/artic_minion.xml
diff --git a/tools/artic/macros.xml b/tools/artic/macros.xml
@@ -1,12 +1,19 @@
 <macros>
-    <token name="@PACKAGE_VERSION@">1.2.3</token>
+    <token name="@TOOL_VERSION@">1.6.0</token>
     <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
+
+    <xml name="requirements">
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">artic</requirement>
+    </requirements>
+    </xml>
+
     <xml name="citations">
         <citations>
             <citation type="bibtex">
                 @misc{githubartic-ncov2019,
-                  author = {Nick Loman and the ZiBRA Project and the ARTIC project},
-                  year = {2017},
+                  author = {@Sam Wilkinson, Nick Loman and the ZiBRA Project and the ARTIC project},
+                  year = {2025},
                   title = {ARTIC toolkit},
                   publisher = {GitHub},
                   journal = {GitHub repository},