# HG changeset patch
# User iuc
# Date 1475511351 14400
# Node ID 025adf89e10dee9556b20815ae0593513f43ac9b
# Parent  247cc24f8b9e231d6e91c7b8974016b529f10852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6

diff -r 247cc24f8b9e -r 025adf89e10d bcftools_gtcheck.xml
--- a/bcftools_gtcheck.xml	Wed Jul 13 10:57:14 2016 -0400
+++ b/bcftools_gtcheck.xml	Mon Oct 03 12:15:51 2016 -0400
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
     <description>Check sample identity</description>
     <macros>
         <token name="@EXECUTABLE@">gtcheck</token>
@@ -83,7 +83,7 @@
             <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" default="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
+            <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)" />
@@ -96,6 +96,7 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="GTs_only" value="" />
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>
diff -r 247cc24f8b9e -r 025adf89e10d macros.xml
--- a/macros.xml	Wed Jul 13 10:57:14 2016 -0400
+++ b/macros.xml	Mon Oct 03 12:15:51 2016 -0400
@@ -339,7 +339,6 @@
         </when>
         <when value="targets_file">
             <expand macro="macro_targets_file">
-               <optional>true</optional>
             </expand>
         </when>
     </conditional>