--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/freyja_variants.xml	Thu Jul 28 09:26:32 2022 +0000
@@ -0,0 +1,73 @@
+<tool id="freyja_variants" name="Freyja: Call variants"
+      version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="@PROFILE@">
+    <description>
+        and get sequencing depth information
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s '$bam_file' 'bam_file' &&
+ln -s '$ref_file' 'ref_file' &&
+freyja variants 
+    'bam_file'
+    --variants variants 
+    --depths '$depths'
+    --ref 'ref_file'
+    ]]></command>
+    <inputs>
+        <param name="bam_file" type="data" format="bam" label="BAM file"
+               help="After primer trimming and alignment to reference genome."/>
+        <param name="ref_file" argument="--ref" type="data" format="fasta"
+               label="Reference sequence file"
+               help="Note that the reference should match the fasta file used for alignment."/>
+    </inputs>
+    <outputs>
+        <data name="variants" format="tabular" label="${tool.name} on ${on_string}: Variant call"
+              from_work_dir="variants.tsv">
+        </data>
+        <data name="depths" format="tabular" label="${tool.name} on ${on_string}: Sequencing depth"
+              from_work_dir="depths.tsv">
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="bam_file" value="test.bam"/>
+            <param name="ref_file" value="NC_045512_Hu-1.fasta"/>
+            <output name="variants" ftype="tabular">
+                <assert_contents>
+                    <has_text text="REF_CODON"/>
+                    <has_text text="NC_045512.2"/>
+                </assert_contents>
+            </output>
+            <output name="depths" ftype="tabular">
+                <assert_contents>
+                    <has_text text="NC_045512.2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Information about **freyja variants** method
+============================================
+
+The method uses both samtools and iVar. 
+
+.. class:: warningmark
+
+   Note that the reference should match the fasta file used for alignment. 
+
+Outputs
+=======
+
+We get both variant call and sequencing depth information with this command.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>