--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/std.xml	Tue Aug 05 09:21:07 2025 +0000
@@ -0,0 +1,66 @@
+<tool id="pimento_std" name="PIMENTO Standard primer matching" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENSE@">
+    <description>Finds best-matching primers in reads using a fuzzy search against a standard primer library</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        #if $primers:
+            mkdir primers &&
+            cp '$primers' primers &&
+            pimento std -i '$input_reads' -p primers --minimum_primer_threshold $minimum_primer_threshold $merged -o sample
+        #else
+            pimento std -i '$input_reads' --minimum_primer_threshold $minimum_primer_threshold $merged -o sample
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="input_reads" type="data" label="Input reads" format="fastqsanger.gz"/>
+        <param name="primers" type="data" label="Input standard primers" format="fasta" optional="true"/>
+        <param argument="--minimum_primer_threshold" type="float" value="0.6" min="0.1" max="1.0" label="Minimum primer threshold" help="Any primers with a read proportion lower than this threshold are disregarded"/>
+        <param argument="--merged" type="boolean" truevalue="--merged" falsevalue="" help="Necessary if the input sequence file is made up of merged paired-end or single-end reads"/>
+    </inputs>    
+    <outputs>
+        <data name="fasta_output" label="${tool.name} on ${on_string}: FASTA containing best found single or pairs of primers" format="fasta" from_work_dir="sample_std_primers.fasta"/>
+        <data name="best_found_primers" label="${tool.name} on ${on_string}: Best found primers" format="txt" from_work_dir="sample_std_primer_out.txt"/>
+        <data name="searched_primers" label="${tool.name} on ${on_string}: Every single searched primer" format="txt" from_work_dir="all_standard_primer_proportions.txt"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="3">
+            <param name="input_reads" value="test.fastq.gz"/>
+            <param name="minimum_primer_threshold" value="0.6"/>
+            <param name="merged" value="true"/>
+            <output name="fasta_output">
+                <assert_contents>
+                    <has_line line=">341F"/>
+                    <has_line line="CCTACGGGNGGCWGCAG"/>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+            <output name="best_found_primers">
+                <assert_contents>
+                    <has_line line="V3-V4"/>
+                    <has_line line="341F: 0.984"/>
+                    <has_line line="805R: 0.948"/>
+                </assert_contents>
+            </output>
+            <output name="searched_primers">
+                <assert_contents>
+                    <has_line line="V3;341F:0.984"/>
+                    <has_line line="V3;338F:0.0"/>
+                    <has_n_lines n="148"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[ 
+        Runs the standard primer matching strategy for primer inference. A library
+        of standard primers will be searched in input reads using fuzzy regex to
+        identify primers with high degrees of proportions. The best single, or pair,
+        of primers found will be outputted into a FASTA file (provided any were
+        indeed found). PIMENTO comes with its own standard primer library which will
+        be used as a default. Users can however give their own custom input library,
+        or extend the default library to suit their needs.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>