# HG changeset patch
# User sanbi-uwc
# Date 1537264258 14400
# Node ID f25ff17454f4ce2b2e9d05d24a4fac10c9a04a8c
# Parent  03af7e3e3b2feac05f1edfe518d2738ed8a47140
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty

diff -r 03af7e3e3b2f -r f25ff17454f4 shapeit_phase.xml
--- a/shapeit_phase.xml	Tue Sep 18 01:54:33 2018 -0400
+++ b/shapeit_phase.xml	Tue Sep 18 05:50:58 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="shapeit_phase" name="shapeit_phase" version="0.9.0">
+<tool id="shapeit_phase" name="shapeit_phase" version="0.10.0">
     <description>genomic data with or without reference panel</description>
 
     <requirements>
@@ -10,7 +10,16 @@
 
     <command><![CDATA[
         #if str($use_ref_panel.use_ref_panel_select) == "use_ref_panel_yes" and str($use_ref_panel.ref_panel_from_table.ref_panel_from_table_select) == "ref_panel_from_table_yes" and str($input_files.input_type_select) == 'plink_bed_bim_fam_list':
-          PART=`head -1 myfile.bim | cut -f1` && 
+          ln -s '${input_files.plink_bed_etc_list[0]}' input.plink_bed &&
+          ln -s '${input_files.plink_bed_etc_list[1]}' input.plink_bim && 
+          ln -s '${input_files.plink_bed_etc_list[2]}' input.plink_fam &&
+          echo "BED file" &&
+          ls -l input.plink_bed &&
+          echo "BIM file" &&
+          head -2 input.plink_bim && 
+          echo "FAM file" &&
+          head -2 input.plink_fam &&
+          PART=`head -1 input.plink_bim | cut -f1` && 
           echo "Working on PART: \$PART" &&
           REF_DIR='${use_genetic_map.genetic_map_from_table.map_from_table.fields.path}' &&
           REF_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.reference_prefix}' &&
@@ -42,15 +51,6 @@
           #for $dat in $input_files.plink_bed_etc_list:
              echo NAME '${dat.name}' &&
           #end for
-          ln -s '${input_files.plink_bed_etc_list[0]}' input.plink_bed &&
-          ln -s '${input_files.plink_bed_etc_list[1]}' input.plink_bim && 
-          ln -s '${input_files.plink_bed_etc_list[2]}' input.plink_fam &&
-          echo "BED file" &&
-          ls -l input.plink_bed &&
-          echo "BIM file" &&
-          head -2 input.plink_bim && 
-          echo "FAM file" &&
-          head -2 input.plink_fam &&
         #end if
 
         shapeit