Mercurial > repos > iuc > snippy

diff snippy.xml @ 11:5bbf9eada9c2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
author iuc
date Wed, 11 Mar 2020 03:50:47 -0400
parents e4d0231d8595
children fa016f1eea1a
line wrap: on
line diff
--- 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>