# HG changeset patch
# User sanbi-uwc
# Date 1537266490 14400
# Node ID b69dadabf6716ce210f9072d25666443a9aca829
# Parent  557cc7904a2b2f50a935c4654b504c69d5417ca6
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty

diff -r 557cc7904a2b -r b69dadabf671 shapeit_phase.xml
--- a/shapeit_phase.xml	Tue Sep 18 06:12:53 2018 -0400
+++ b/shapeit_phase.xml	Tue Sep 18 06:28:10 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="shapeit_phase" name="shapeit_phase" version="0.11.0">
+<tool id="shapeit_phase" name="shapeit_phase" version="0.12.0">
     <description>genomic data with or without reference panel</description>
 
     <requirements>
@@ -9,7 +9,7 @@
     </stdio>
 
     <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($input_files.input_type_select) == 'plink_bed_bim_fam_list':
+        #if str($input_files.input_type_select) == 'plink_bed_bim_fam_list':
           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 '${input_files.plink_bed_etc_list[2]}' input.plink_fam &&
@@ -21,9 +21,13 @@
           head -2 input.plink_fam &&
           PART=`head -1 input.plink_bim | cut -f1` && 
           echo "Working on PART: \$PART" &&
-          REF_DIR='${use_genetic_map.genetic_map_from_table.map_from_table.fields.path}' &&
-          REF_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.reference_prefix}' &&
-          SAMPLE_PREFIX="\$REF_DIR/${use_genetic_map.genetic_map_from_table.map_from_table.fields.sample_prefix}" &&
+        #else
+          PART=''
+        #end if 
+        #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":
+          REF_DIR='${use_ref_panel.ref_panel_from_table.ref_from_table.fields.path}' &&
+          REF_PREFIX='${use_ref_panel.ref_panel_from_table.ref_from_table.fields.reference_prefix}' &&
+          SAMPLE_PREFIX="\$REF_DIR/${use_ref_panel.ref_panel_from_table.ref_from_table.fields.sample_prefix}" &&
           SAMPLE=`ls \$SAMPLE_PREFIX*.sample` &&
           if [ ! -f "\$SAMPLE" ] ; then
             echo "Failed to find valid sample file at \$SAMPLE" >&2 && 
@@ -39,8 +43,11 @@
             echo "Failed to find valid .legend file at \$LEGEND" >&2 &&
             exit 1 ;
           fi &&
+        #end if
+        #if $use_genetic_map.genetic_map_select == "use_genetic_map_yes" && $use_genetic_map.genetic_map_from_table.genetic_map_from_table_select == "genetic_map_from_table_yes":
+          MAP_DIR='${use_genetic_map.genetic_map_from_table.map_from_table.fields.path}' &&
           MAP_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.map_prefix}' &&
-          MAP=`ls \${REF_DIR}/\${MAP_PREFIX}\${PART}_*` &&
+          MAP=`ls \${MAP_DIR}/\${MAP_PREFIX}\${PART}_*` &&
           if [ ! -f "\${MAP}" ] ; then
             echo "Failed to find valid map file at \${MAP}" >&2 &&
             exit 1 ; 
@@ -49,7 +56,7 @@
         #if $input_files.input_type_select == "plink_bed_bim_fam_list":
           echo "COLLECTION NAME:" ${input_files.plink_bed_etc_list.name} &&
           #for $dat in $input_files.plink_bed_etc_list:
-             echo NAME '${dat.name}' &&
+             echo Processing NAME '${dat.name}' &&
           #end for
         #end if