--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snvtocnv.xml	Sun Mar 07 23:19:59 2021 +0000
@@ -0,0 +1,76 @@
+<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.7.0">
+    <description>
+    </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="3.0.0">sequenza-utils</requirement>
+        <requirement type="package" version="3.0.0">r-sequenza</requirement>
+        <requirement type="package" version="1.6.6">r-optparse</requirement>
+        <requirement type="package" version="1.24.0">bioconductor-biocparallel</requirement>
+        <requirement type="package" version="1.3.0">r-tidyverse</requirement>
+        <requirement type="package" version="2021a=he74cb21_0">tzdata</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occured" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+    @pipefail@
+    sequenza-utils snp2seqz -v '$input_snvs'  -gc $refwig -o sample.seqz.gz &&
+    sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o '$wiggle' &&
+    Rscript $__tool_directory__/segmentation_sequenza.R
+            -i '$wiggle'
+            -s sample
+            -O test &&
+    Rscript $__tool_directory__/sequenza_to_hrdtools_input.R
+            -i test/sample_segments.txt
+            -s test/sample_alternative_solutions.txt
+            -o '$cnvs'
+    ]]></command>
+    <inputs>
+        <param name="refwig" type="data" format="txt" label="GC wigle of reference genome"/>
+        <param name="input_snvs" type="data" format="vcf" label="SNVs to process in a vcf file"/>
+    </inputs>
+    <outputs>
+        <data name="wiggle" format="txt" label="binned wiggle" />
+        <data name="sample_segment" format="txt" label="sample segments" from_work_dir="test/sample_segments.txt" />
+        <data name="alt_solutions" format="txt" label="alternate solutions" from_work_dir="test/sample_alternative_solutions.txt" />
+        <data name="cnvs" format="tabular" label="Annotated CNVs" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_snvs" value="hg19_chr22.vcf" ftype="vcf" />
+            <param name="refwig" value="hg19.GCref.txt" />
+            <output name="cnvs" file="hg19.cnv.tab" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input_snvs" value="hg38_chr22.vcf" ftype="vcf" />
+            <param name="refwig" value="hg38.GCref.txt" />
+            <output name="cnvs" file="hg38.cnv.tab" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+
+snvtocnv
+============================
+
+Analyze 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.
+
+    
+Inputs
+--------
+
+A GC wigle of genome index generated with the tool "create GC_wiggle of reference genome"
+available from this galaxy wrapper
+
+A vcf file of somatic *single* nucleotide variations observed in a tumor sample
+
+
+    </help>
+    <citations>
+        <citation type="doi">10.1093/annonc/mdu479</citation>
+    </citations>
+</tool>