--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pacu_map.xml	Tue Aug 13 13:44:35 2024 +0000
@@ -0,0 +1,106 @@
+<tool id="pacu_map" name="PACU - mapping" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Map ONT / Illumina reads to a reference genome for PACU</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro="requirements" />
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        PACU_map
+
+        ## FASTA input
+        --ref-fasta '$ref_fasta'
+        --ref-fasta-name '$ref_fasta.element_identifier'
+
+        ## FASTQ input
+        --read-type $fastq_tech.read_type
+        #if str($fastq_tech.read_type) == 'illumina':
+            --fastq-illumina $fastq_tech.fastq_illumina_1 $fastq_tech.fastq_illumina_2
+            --fastq-illumina-names '$fastq_tech.fastq_illumina_1.element_identifier' '$fastq_tech.fastq_illumina_2.element_identifier'
+        #elif str($fastq_tech.read_type) == 'ont':
+            --fastq-ont $fastq_tech.fastq_ont
+            --fastq-ont-name '$fastq_tech.fastq_ont.element_identifier'
+        #end if
+
+        ## Output
+        --output '$bam'
+
+        ## Other options
+        $trim
+        --dir-working \$PWD
+        --threads \${GALAXY_SLOTS}
+        ]]>
+    </command>
+    <inputs>
+        <param argument="--ref-fasta" type="data" format="fasta" label="Reference genome"/>
+        <conditional name="fastq_tech">
+            <param argument="--read-type" type="select" label="FASTQ type">
+                <option value="illumina">Illumina paired-end reads</option>
+                <option value="ont">ONT single-end reads</option>
+            </param>
+            <when value="illumina">
+                <param name="fastq_illumina_1" type="data" format="fastq,fastqsanger.gz" label="Forward reads"/>
+                <param name="fastq_illumina_2" type="data" format="fastq,fastqsanger.gz" label="Reverse reads"/>
+            </when>
+            <when value="ont">
+                <param name="fastq_ont" type="data" format="fastq,fastqsanger.gz" label="ONT reads"/>
+            </when>
+        </conditional>
+        <param argument="--trim" type="boolean" label="Trim reads" checked="true" truevalue="--trim" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="bam" format="bam" label="Mapping on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <!-- The line differences correspond to the three commands in the SAM header -->
+            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+            <conditional name="fastq_tech">
+                <param name="read_type" value="ont"/>
+                <param name="fastq_ont" value="TIAC1151-ont.gz"/>
+            </conditional>
+            <param name="trim" value="false" />
+            <output name="bam" ftype="bam" file="mapped_reads-ont.bam" lines_diff="6"/>
+        </test>
+        <test>
+            <!-- The line differences correspond to the three commands in the SAM header -->
+            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+            <conditional name="fastq_tech">
+                <param name="read_type" value="illumina"/>
+                <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
+                <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
+            </conditional>
+            <param name="trim" value="false" />
+            <output name="bam" ftype="bam" file="mapped_reads-ilmn.bam" lines_diff="6"/>
+        </test>
+                <test>
+            <!-- The line differences correspond to the three commands in the SAM header -->
+            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+            <conditional name="fastq_tech">
+                <param name="read_type" value="ont"/>
+                <param name="fastq_ont" value="TIAC1151-ont.gz"/>
+            </conditional>
+            <param name="trim" value="true" />
+            <output name="bam" ftype="bam" file="mapped_reads_trimmed-ont.bam" lines_diff="6"/>
+        </test>
+        <test>
+            <!-- The line differences correspond to the three commands in the SAM header -->
+            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+            <conditional name="fastq_tech">
+                <param name="read_type" value="illumina"/>
+                <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
+                <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
+            </conditional>
+            <param name="trim" value="true" />
+            <output name="bam" ftype="bam" file="mapped_reads_trimmed-ilmn.bam" lines_diff="6"/>
+        </test>
+    </tests>
+    <help>
+        This script maps Illumina or ONT reads to an input reference genome in FASTA format.
+        It also writes a custom tag to the BAM file to propagate the sample name to PACU within Galaxy.
+        The sample name is derived from the name of the input FASTQ files.
+    </help>
+    <expand macro="citations"/>
+</tool>