--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wigToBigWig.xml	Mon Jun 05 02:54:00 2023 +0000
@@ -0,0 +1,38 @@
+<tool id="edu.tamu.cpt.util.wigToBigWig" name="Wig to BigWig" version="19.1.0.0" profile="16.04">
+    <description>CPT version accepts fasta input for genome lengths.</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>cpt-macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="377">ucsc-wigtobigwig</requirement>
+    </expand>
+    <command detect_errors="aggressive"><![CDATA[
+python '$__tool_directory__/fasta_len.py' '$genomes' > 'chrom.len';
+
+grep -v "^track" '$wigFile' |
+wigToBigWig -clip stdin chrom.len '$bigwig'
+]]></command>
+    <inputs>
+        <param name="wigFile" type="data" format="wig" label="Wig File"/>
+        <param name="genomes" type="data" format="fasta" label="Fasta File" help="File containing fasta sequences referenced by wig file"/>
+    </inputs>
+    <outputs>
+        <data format="bigwig" name="bigwig"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="wigFile" value="T7_BW_I_REBASE.wig"/>
+            <param name="genomes" value="T7_CLEAN.fasta"/>
+            <output name="bigwig" value="T7_BW_I_REBASE.bigwig"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Convert wig to bigWig
+]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/bioinformatics/btq351</citation>
+    </expand>
+</tool>