--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnplot.xml	Fri Feb 21 21:26:13 2025 +0000
@@ -0,0 +1,78 @@
+<tool id="merquryfk_cnplot" name="MerquryFK CNplot" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>Creates copy-number spectrum plots from a genomic read k-mer table and its assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s $reads input.ktab &&
+        ln -s $assembly input.fastq &&
+        ln -s $fastk_ktab_files ktab_files.tar.gz &&
+        tar -xf ktab_files.tar.gz -C '.' &&
+        mv ktabfiles/.*.ktab* .input.ktab.1  &&
+        CNplot
+        @PLOTS@
+        @MEASURE@
+        @GRAPHS@
+        $pdf
+        -T\${GALAXY_SLOTS:-1}
+        input.ktab
+        input.fastq
+        output
+    ]]></command>
+    <inputs>
+        <param name="reads" type="data" format="fastk_ktab" label="K-mer table (ktab) obtained from FastK tool"/>
+        <param name="fastk_ktab_files" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of all intermediate Ktab file from FastK"/>
+        <param name="assembly" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Assembly of genome" help="Must be same genome as the K-mer table was generated from"/>
+        <expand macro="plots"/>
+        <expand macro="sizes"/>
+        <expand macro="graphs"/>
+        <expand macro="pdf"/>
+    </inputs>
+    <outputs>
+        <collection name="outputs_png" type="list" label="${tool.name} on ${on_string}: PNG figures">
+            <filter>pdf is not True</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).png" format="png"/>
+        </collection>
+        <collection name="outputs_pdf" type="list" label="${tool.name} on ${on_string}: PDF figures">
+            <filter>pdf is True</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).pdf" format="pdf"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="reads" value="maternal.ktab"/>
+            <param name="fastk_ktab_files" ftype="fastk_ktab_tar" value="cnplot_ktab.tar.gz"/>
+            <param name="assembly" value="maternal.fastq"/>
+            <param name="width" value="6.0"/>
+            <param name="height" value="4.5"/>
+            <param name="graphs" value="-l,-f,-s"/>
+            <param name="pdf" value="False"/>
+            <conditional name="measure">
+                <param name="measurement" value="absolute"/>
+                <param name="max_x" value="2"/>
+                <param name="max_y" value="1"/>
+            </conditional>
+            <output_collection name="outputs_png" count="3"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="reads" value="maternal.ktab"/>
+            <param name="fastk_ktab_files" ftype="fastk_ktab_tar" value="cnplot_ktab.tar.gz"/>
+            <param name="assembly" value="maternal.fastq"/>
+            <param name="width" value="6.0"/>
+            <param name="height" value="4.5"/>
+            <param name="graphs" value="-l,-f,-s"/>
+            <param name="pdf" value="True"/>
+            <conditional name="measure">
+                <param name="measurement" value="absolute"/>
+                <param name="max_x" value="2"/>
+                <param name="max_y" value="1"/>
+            </conditional>
+            <output_collection name="outputs_pdf" count="3"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Given a k-mer table, produced by FastK, for a read data set, and an assembly of the same genome, CNplot produces copy-number spectrum plots for the pair. 
+            ]]></help>
+    <expand macro="citation"/>
+</tool>
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