# HG changeset patch
# User iuc
# Date 1583913047 14400
# Node ID 5bbf9eada9c260aa8d6e09bb89abdf4540cab18e
# Parent  3fe8ef358d663a07996ad4c72fa0532bf20bbcf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"

diff -r 3fe8ef358d66 -r 5bbf9eada9c2 macros.xml
--- a/macros.xml	Thu Jan 30 18:18:38 2020 -0500
+++ b/macros.xml	Wed Mar 11 03:50:47 2020 -0400
@@ -57,7 +57,7 @@
         </conditional>
     </xml>
 
-    <token name="@VERSION@">4.4.5</token>
+    <token name="@VERSION@">4.5.0</token>
 
     <xml name="citations">
       <citations>
diff -r 3fe8ef358d66 -r 5bbf9eada9c2 snippy-core.xml
--- a/snippy-core.xml	Thu Jan 30 18:18:38 2020 -0500
+++ b/snippy-core.xml	Wed Mar 11 03:50:47 2020 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy2">
+<tool id="snippy_core" name="snippy-core" version="@VERSION@">
     <description>
         Combine multiple Snippy outputs into a core SNP alignment
     </description>
diff -r 3fe8ef358d66 -r 5bbf9eada9c2 snippy.xml
--- a/snippy.xml	Thu Jan 30 18:18:38 2020 -0500
+++ b/snippy.xml	Wed Mar 11 03:50:47 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="snippy" name="snippy" version="@VERSION@+galaxy2">
+<tool id="snippy" name="snippy" version="@VERSION@">
   <description>
       Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
     </description>
@@ -153,8 +153,8 @@
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />
-            <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
-            <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
+            <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
+            <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
         </test>
 
         <test>            <!-- test 1 - fasta ref one snp -->
@@ -168,8 +168,8 @@
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />
-            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
-            <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
+            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
+            <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
         </test>
 
         <test>            <!-- test 2 - fasta ref one snp paired_collection -->
@@ -187,8 +187,8 @@
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />
-            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
-            <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
+            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
+            <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
         </test>
 
         <test>            <!-- test 3 - fasta ref one snp single -->
@@ -201,8 +201,8 @@
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />
-            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
-            <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
+            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
+            <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
         </test>
 
         <test>            <!-- test 4 - reference source as cached -->
@@ -215,8 +215,8 @@
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />
-            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
-            <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
+            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
+            <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
         </test>
     </tests>
 
diff -r 3fe8ef358d66 -r 5bbf9eada9c2 snippy_clean_full_aln.xml
--- a/snippy_clean_full_aln.xml	Thu Jan 30 18:18:38 2020 -0500
+++ b/snippy_clean_full_aln.xml	Wed Mar 11 03:50:47 2020 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="snippy_clean_full_aln" name="snippy-clean_full_aln" version="@VERSION@+galaxy0">
+<tool id="snippy_clean_full_aln" name="snippy-clean_full_aln" version="@VERSION@">
     <description>
         Replace any non-standard sequence characters in snippy 'core.full.aln' file.
     </description>