--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequenza_index.xml	Sun Mar 07 23:19:59 2021 +0000
@@ -0,0 +1,63 @@
+<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="0.7.0">
+    <description>
+    </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="3.0.0">sequenza-utils</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occured" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+    @pipefail@
+    sequenza-utils gc_wiggle  --fasta $reference -o $refwig -w $window
+    ]]></command>
+    <inputs>
+        <param name="reference" type="data" format="fasta" label="Genome in fasta format"
+               help="the fasta genome whose GC content will be indexed"/>
+        <param name="window" type="integer" value="50" label="window size" help="The size of the wiggle for GC content calculation" />
+     </inputs>
+    <outputs>
+        <data name="refwig" format="txt" label="reference_wig" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="window" value="100" ftype="vcf" />
+            <param name="reference" value="hg19_chr22.fa.gz" />
+            <output name="refwig" file="hg19.GCref.txt" ftype="txt" />
+        </test>
+        <test>
+            <param name="window" value="100" ftype="vcf" />
+            <param name="reference" value="hg38_chr22.fa.gz" />
+            <output name="refwig" file="hg38.GCref.txt" ftype="txt" />
+        </test>
+
+    </tests>
+    <help>
+
+snvtocnv
+============================
+
+Analyzes genomic sequencing data from paired normal-tumor samples, including
+cellularity and ploidy estimation; mutation and copy number (allele-specific and total
+copy number) detection, quantification and visualization.
+
+This tools builds the GC wigle index of the reference genome required to perform analysis
+of the somatic single nucleotide variations using the tool "Infer CNVs from SNVs"
+
+    
+Inputs
+--------
+
+The reference genome in a fasta format
+
+*Warning* the genome fasta must be sorted according to the chromosomes
+(e.g. chr1, chr2, .. chr21, chr22)
+
+    </help>
+    <citations>
+        <citation type="doi">10.1093/annonc/mdu479</citation>
+    </citations>
+</tool>