--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/auto.xml	Tue Aug 05 09:20:38 2025 +0000
@@ -0,0 +1,44 @@
+<tool id="pimento_auto" name="PIMENTO Primer cutoff prediction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENSE@">
+    <description>Infers primers by predicting optimal cutoff points from read conservation patterns</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        pimento auto -i '$input' -st '$strand' -o sample
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" label="Input reads" format="fastqsanger.gz"/>
+        <param name="strand" type="select" label="Strand" format="fastqsanger.gz">
+            <option value="F">Forward</option>
+            <option value="R">Reverse</option>
+            <option value="FR">Both, forward and reverse</option>
+        </param>
+    </inputs>    
+    <outputs>
+        <data name="output" label="${tool.name} on ${on_string}: Automatically inferred primers" format="fasta" from_work_dir="sample_auto_primers.fasta"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="test.fastq.gz"/>
+            <param name="strand" value="FR"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line=">F_auto"/>
+                    <has_line line="CCTACGGGDGGCWGCAGT"/>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[ 
+        Runs the primer cutoff strategy for primer inference. Using patterns of
+        base-conservation values for input reads, this strategy identifies potential
+        cutoff points where a primer sequence could end. An optimal choice of cutoff
+        based on the change in base-conservation before and after a cutoff is then
+        made. Finally a consensus sequence is generated using this cutoff point and
+        the input reads, which are saved to an output FASTA file.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>