# HG changeset patch
# User sanbi-uwc
# Date 1537285684 14400
# Node ID 42bafd3c5a83e962830f4c580d1c1e61f09da088
# Parent  d3515c2a3f51b3f7b3814bd7e2ab1fd077b66d66
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 75ae96395b13aafb20f82b220c4d14ac484b6767-dirty

diff -r d3515c2a3f51 -r 42bafd3c5a83 shapeit_phase.xml
--- a/shapeit_phase.xml	Tue Sep 18 09:49:26 2018 -0400
+++ b/shapeit_phase.xml	Tue Sep 18 11:48:04 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="shapeit_phase" name="shapeit_phase" version="0.17.0">
+<tool id="shapeit_phase" name="shapeit_phase" version="0.18.0">
     <description>genomic data with or without reference panel</description>
     <requirements>
         <requirement type="package" version="2.r837">shapeit</requirement>
@@ -127,14 +127,15 @@
           #else if $use_filters.filter_individuals == "include_individuals":
             --include-ind $use_filters.include_inviduals_file
           #end if
-          #if $use_filters.filter_individuals == "exclude_SNPs":
-            --exclude-snp $use_filters.exclude_SNPs_file
-          #else if $use_filters.filter_SNPs == "include_SNPs":
-            --include-snp $use_filters.include_SNPs_file
+          #if $use_filters.filter_SNPs.filter_SNPs_select == "exclude_SNPs":
+            --exclude-snp $use_filters.filter_SNPs.exclude_SNPs_file
+          #else if $use_filters.filter_SNPs.filter_SNPs_select  == "include_SNPs":
+            --include-snp $use_filters.filter_SNPs.include_SNPs_file
           #end if
         #end if
 
         #if $use_advanced_parameters.use_advanced_parameters_select == "use_advanced_parameters_yes":
+          $use_advanced_parameters.duohmm
           #if $use_advanced_parameters.chrX == "chrX_yes":
             --chrX
           #end if
@@ -306,6 +307,7 @@
         </param>
 
         <when value="use_advanced_parameters_yes">
+          <param argument="--duohmm" type="boolean" truevalue="--duohmm" falsevalue="" />
           <param name="chrX" type="select" label="Use X chromosomal genotypes?">
             <option value="chrX_yes">Yes</option>
             <option value="chrX_no" selected="True">No</option>
@@ -425,16 +427,16 @@
 
           <conditional name="filter_SNPs">
             <param name="filter_SNPs_select" type="select" label="Do you want to filter SNPs?">
-              <option value="no_individual_filter" selected="True">No filtering</option>
+              <option value="no_SNPs_filter" selected="True">No filtering</option>
               <option value="exclude_SNPs">Exclude list of SNPs</option>
               <option value="include_SNPs">Limit list of SNPs</option>
             </param>
             <when value="no_individual_filter"></when>
             <when value="exclude_SNPs">
-              <param name="exclude_inviduals_file" type="data" format="txt" label="Specify file with excluded SNPs (.exc)"/>
+              <param name="exclude_SNPs_file" type="data" format="txt" label="Specify file with excluded SNPs (.exc)"/>
             </when>
             <when value="include_SNPs">
-              <param name="include_inviduals_file" type="data" format="txt" label="Specify file with limited SNPs (.inc)"/>
+              <param name="include_SNPs_file" type="data" format="txt" label="Specify file with limited SNPs (.inc)"/>
             </when>
           </conditional>
         </when>