# HG changeset patch
# User artbio
# Date 1653066474 0
# Node ID e0724d649885e438a11c05e4653eb9fd969c7ace
# Parent  d2833cfb3f088b50ca2bf3d10367ed7754bef70e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 116f2555558a283190cd1dd60ee25b359bcda51e

diff -r d2833cfb3f08 -r e0724d649885 sequenza_index.xml
--- a/sequenza_index.xml	Thu May 19 20:35:24 2022 +0000
+++ b/sequenza_index.xml	Fri May 20 17:07:54 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="0.7.0">
+<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="3.0.0+galaxy1">
     <description>
     </description>
     <macros>
@@ -20,18 +20,18 @@
         <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" />
+        <data name="refwig" format="wig" 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" />
+            <output name="refwig" file="hg19.GCref.txt" ftype="wig" />
         </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" />
+            <output name="refwig" file="hg38.GCref.txt" ftype="wig" />
         </test>
 
     </tests>
diff -r d2833cfb3f08 -r e0724d649885 snvtocnv.xml
--- a/snvtocnv.xml	Thu May 19 20:35:24 2022 +0000
+++ b/snvtocnv.xml	Fri May 20 17:07:54 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="snvtocnv" name="Infer CNVs from SNVs" version="3.0.0+galaxy0">
+<tool id="snvtocnv" name="Infer CNVs from SNVs" version="3.0.0+galaxy1">
     <description>
     </description>
     <macros>
@@ -34,9 +34,9 @@
         <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="wiggle" format="wig" label="binned wiggle" />
+        <data name="sample_segment" format="tabular" label="sample segments" from_work_dir="test/sample_segments.txt" />
+        <data name="alt_solutions" format="tabular" label="alternate solutions" from_work_dir="test/sample_alternative_solutions.txt" />
         <data name="cnvs" format="tabular" label="Annotated CNVs" />
         <data name="chrom_depths" format="pdf" label="Chromosomes sequencing depth" from_work_dir="test/sample_chromosome_depths.pdf"/>
         <data name="chrom_view" format="pdf" label="Chromosomes views" from_work_dir="test/sample_chromosome_view.pdf"/>