Mercurial > repos > iuc > colibread_discosnp_rad

changeset 2:9ee3bf979757 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 45e32ab41e7cdc4e3dabe87f074f052667c22574"
author iuc
date Wed, 22 Jan 2020 17:26:07 -0500
parents 62a7874355b7
children 2af5a5ca9c87
files discosnp_RAD.xml test-data/discosnpRAD/vcf_file.vcf
diffstat 2 files changed, 7 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/discosnp_RAD.xml	Wed Sep 05 09:01:59 2018 -0400
+++ b/discosnp_RAD.xml	Wed Jan 22 17:26:07 2020 -0500
@@ -60,7 +60,13 @@
           <param name="k" value="31"/>
           <param name="b" value="2"/>
           <output name="fasta" file="discosnpRAD/fasta.fa"/>
-          <output name="vcf" file="discosnpRAD/vcf_file.vcf" compare="diff" lines_diff="2"/>
+          <output name="vcf">
+              <assert_contents>
+                  <has_n_lines n="8"/>
+                  <has_text text="Ty=SNP;Rk=0;UL=23;UR=39;CL=.;CR=.;Genome=.;Sd=."/>
+                  <has_text text="0/1:84:604,15,604:42,42:0,0"/>
+              </assert_contents>
+          </output>
       </test>
   </tests>
 
--- a/test-data/discosnpRAD/vcf_file.vcf	Wed Sep 05 09:01:59 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-cluster_0_size_4	.	SNP_higher_path_1	A	T	.	.	Ty=SNP;Rk=0;UL=23;UR=39;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/1:84:604,15,604:42,42:0,0
-cluster_0_size_4	.	SNP_higher_path_3	A	C	.	.	Ty=SNP;Rk=0;UL=23;UR=0;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/1:84:604,15,604:42,42:0,0
-cluster_1_size_6	.	SNP_higher_path_2	C	T	.	.	Ty=SNP;Rk=0;UL=8;UR=0;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/1:98:702,15,702:49,49:0,0
-cluster_1_size_6	.	SNP_higher_path_6	C	G	.	.	Ty=SNP;Rk=0;UL=1;UR=8;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/1:98:702,15,702:49,49:0,0
-cluster_1_size_6	.	SNP_higher_path_7	C	T	.	.	Ty=SNP;Rk=0;UL=1;UR=16;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0|1:98:702,15,702:49,49:0,0
-cluster_1_size_6	.	SNP_higher_path_7	C	G	.	.	Ty=SNP;Rk=0;UL=1;UR=16;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0|1:98:702,15,702:49,49:0,0
-cluster_2_size_4	.	SNP_higher_path_4	A	G	.	.	Ty=SNP;Rk=0;UL=51;UR=0;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/1:88:632,15,632:44,44:0,0
-cluster_2_size_4	.	SNP_higher_path_5	A	C	.	.	Ty=SNP;Rk=0;UL=5;UR=51;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/1:88:632,15,632:44,44:0,0