diff bcftools_gtcheck.xml @ 16:a29a2f40b665 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

--- a/bcftools_gtcheck.xml	Sat Jul 23 13:37:10 2022 +0000
+++ b/bcftools_gtcheck.xml	Tue Sep 20 13:09:16 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Check sample identity</description>
     <macros>
         <token name="@EXECUTABLE@">gtcheck</token>
@@ -47,10 +47,6 @@
 
 ${section.all_sites}
 
-#if $section.GTs_only:
-  --GTs-only '${section.GTs_only}'
-#end if
-
 ${section.homs_only}
 
 #if $section.plot:
@@ -85,7 +81,6 @@
             <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
                    help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
             <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
-            <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
             <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
             <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />
             <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" />
@@ -98,10 +93,9 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="GTs_only" value="99" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text_matching expression="CN\t3\t10\t0\tNA00002\tNA00001"/>
+                    <has_text_matching expression="DC\tNA00002\tNA00001\t6"/>
                 </assert_contents>
             </output>
         </test>