# HG changeset patch
# User sanbi-uwc
# Date 1536959356 14400
# Node ID 4a048227b86f2616bfe30dfdbd7c3d1c09c6e9ca
# Parent  4eccc085e9fe88f4350c37225961ebbd94f33da5
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 6dfd47f8de029246dd63d60f24ed685a13f8a2ff-dirty

diff -r 4eccc085e9fe -r 4a048227b86f shapeit_phase.xml
--- a/shapeit_phase.xml	Fri Sep 14 03:11:54 2018 -0400
+++ b/shapeit_phase.xml	Fri Sep 14 17:09:16 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="shapeit_phase" name="shapeit_phase" version="0.2.0">
+<tool id="shapeit_phase" name="shapeit_phase" version="0.3.0">
     <description>genomic data with or without reference panel</description>
 
     <requirements>
@@ -25,7 +25,7 @@
             echo "Failed to find valid map file at \${MAP}" >&2 &&
             exit 1 ; 
           fi &&
-        # end 
+        #end if
 
         shapeit
 
@@ -48,7 +48,7 @@
         #end if
 
         #if $use_genetic_map.use_genetic_map_select == "use_genetic_map_yes":
-          #if $use_genetic_map.genetic_map_from_table == "genetic_map_from_table_yes":
+          #if $use_genetic_map.genetic_map_from_table_select == "genetic_map_from_table_yes":
             --input-map \$MAP
           else:
             --input-map $use_genetic_map.genetic_map
@@ -58,10 +58,10 @@
         #end if
 
         #if $use_ref_panel.use_ref_panel_select == "use_ref_panel_yes":
-          #if $use_ref_panel.ref_panel_from_table == "ref_panel_from_table_yes":
+          #if $use_ref_panel.ref_panel_from_table_select == "ref_panel_from_table_yes":
             --input-ref \$HAP \$LEGEND \$SAMPLE
           #else
-            --input-ref $use_ref_panel.ref_panel_haps $use_ref_panel.ref_panel_legend $use_ref_panel.ref_panel_sample
+            --input-ref $use_ref_panel.ref_panel_from_table.ref_panel_haps $use_ref_panel.ref_panel_from_table.ref_panel_legend $use_ref_panel.ref_panel_from_table.ref_panel_sample
           #end if
           #if $use_ref_panel.disable_mcmc_iterations == "disable_mcmc_iterations_yes":
             --no-mcmc
@@ -399,8 +399,8 @@
     <outputs>
       <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)"/>
       <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)"/>
-      <data name="out_graph" format="text" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"/>
-      <data name="out_log" format="text" label="${tool.name} on ${on_string} logfile (.log)"/>
+      <data name="out_graph" format="txt" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"/>
+      <data name="out_log" format="txt" label="${tool.name} on ${on_string} logfile (.log)"/>
     </outputs>
     <help><![CDATA[
         TODO: Fill in help.