# HG changeset patch
# User artbio
# Date 1613748125 0
# Node ID 15b26e44b18d94ef3a9edd822f0a849ce11c82a3
# Parent  9265faa93098aba502a4f28d0d1a6a9b2d68b6ba
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8-dirty"

diff -r 9265faa93098 -r 15b26e44b18d snvtocnv.xml
--- a/snvtocnv.xml	Fri Feb 19 14:56:45 2021 +0000
+++ b/snvtocnv.xml	Fri Feb 19 15:22:05 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.2">
+<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.2.1">
     <description>
     </description>
     <macros>
@@ -23,8 +23,8 @@
     #else:
         ln -s $input_snvs input_snv.vcf &&
     #end if
-    sequenza-utils gc_wiggle  --fasta reference.fa -o reference.gc50Base.wig.gz -w 50 &&
-    sequenza-utils snp2seqz -v '$input_snvs'  -gc reference.gc50Base.wig.gz -o sample.seqz.gz &&
+    sequenza-utils gc_wiggle  --fasta reference.fa -o $refwig -w 50 &&
+    sequenza-utils snp2seqz -v '$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'
@@ -45,7 +45,8 @@
         </param>
     </inputs>
     <outputs>
-        <data name="wiggle" format="binary" label="binned wiggle" />
+        <data name="refwig" format="txt" label="reference_wig" />
+        <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" />