--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tracy_basecall.xml	Tue Oct 12 14:21:34 2021 +0000
@@ -0,0 +1,67 @@
+<tool id="tracy_basecall" name="tracy Basecall" version="@TOOL_VERSION@+galaxy0" profile="20.09">
+    <description>from Sanger chromatogram tracefile</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        tracy basecall --pratio $pratio --format $format --output '$output' '$tracefile'
+    ]]></command>
+    <inputs>
+        <param name="tracefile" type="data" format="ab1,scf" label="Chromatogram tracefile" />
+        <param argument="--pratio" type="float" label="Peak ratio to call a base" value="0.33" min="0" />
+        <param argument="--format" type="select" label="Output format">
+            <option value="fasta" selected="true">FASTA</option>
+            <option value="fastq">FASTQ</option>
+            <option value="tsv">TSV (tabular)</option>
+            <option value="json">JSON</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" label="tracy basecall on ${on_string}">
+            <change_format>
+                <when input="format" value="fasta" format="fasta"/>
+                <when input="format" value="fastq" format="fastq"/>
+                <when input="format" value="tsv" format="tabular"/>
+                <when input="format" value="json" format="json" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="tracefile" value="input1.ab1" ftype="ab1" />
+            <output name="output" file="output1.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="tracefile" value="input1.ab1" ftype="ab1" />
+            <param name="format" value="json" />
+            <output name="output" file="output1.json" ftype="json" />
+        </test>
+        <test>
+            <param name="tracefile" value="input1.ab1" ftype="ab1" />
+            <param name="pratio" value="0.2" />
+            <output name="output" file="output2.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="tracefile" value="input2.scf" ftype="scf" />
+            <param name="format" value="fasta" />
+            <output name="output" file="output3.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Basecall a chromatogram trace file (using tracy_) and output the primary sequence (highest peak) in FASTQ or FASTA format. If FASTQ
+format is used, the quality scores are Sanger quality scores.
+
+@pratio@
+
+Read more here_
+
+.. _tracy: https://github.com/gear-genomics/tracy
+.. _here: https://www.gear-genomics.com/docs/tracy/cli/#basecalling-a-chromatogram-trace-file
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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