# HG changeset patch
# User jaredgk
# Date 1539727431 14400
# Node ID 15245deda141e897697459e1183dc059e3e9448d
# Parent  3830d29fca6a936295e21a9b7048c7ab31f7d943
Uploaded

diff -r 3830d29fca6a -r 15245deda141 vcf_phase.xml
--- a/vcf_phase.xml	Mon Oct 15 18:15:47 2018 -0400
+++ b/vcf_phase.xml	Tue Oct 16 18:03:51 2018 -0400
@@ -5,40 +5,44 @@
   <requirements>
       <requirement type="package" >pandas</requirement>
       <requirement type="package" >pysam</requirement>
+      <requirement type="package" >beagle</requirement>
       <requirement type="package" >shapeit</requirement>
-      <requirement type="package" >beagle</requirement>
   </requirements>
 
   <command><![CDATA[
     #if $input.is_of_type('vcf_bgzip')
       ln -fs $input input.vcf.gz &&
+      ln -fs $input.metadata.tabix_index input.vcf.gz.tbi &&
     #end if
     #if $input.is_of_type('vcf')
       ln -fs $input input.vcf &&
     #end if
     python $__tool_directory__/vcf_phase.py
+            --phase-algorithm $phase.phase_algorithm
+            --out $output
+            --out-format $out_format
+
             #if $input.is_of_type('vcf_bgzip')
                --vcf input.vcf.gz
             #end if
+
             #if $input.is_of_type('vcf')
                --vcf input.vcf
             #end if
+
             #if $model_file
               --model-file $model_file
               --model $model
             #end if
-            --phase-algorithm $phase.phase_algorithm
-            #if $phase.beagle_burn_iter
-              --beagle-burn-iter $common.beagle_burn_iter
-            #end if
-            #if $phase.beagle_burn_iter
-              --beagle-burn-iter $phase.beagle_burn_iter
-            #end if
+
             #if $phase.phase_algorithm == 'beagle'
               --beagle-path $__tool_data_path__/shared/jars/
               #if $phase.beagle_iter
                 --beagle-iter $phase.beagle_iter
               #end if
+              #if $phase.beagle_burn_iter
+                --beagle-burn-iter $phase.beagle_burn_iter
+              #end if
               #if $phase.beagle_states
                 --beagle-states $phase.beagle_states
               #end if
@@ -58,6 +62,7 @@
                 --beagle-nsteps $phase.beagle_nsteps
               #end if
             #end if
+
             #if $phase.phase_algorithm == 'shapeit'
               #if $phase.shapeit_burn_iter
                 --shapeit-burn-iter $phase.shapeit_burn_iter
@@ -75,26 +80,32 @@
                 --shapeit-window $phase.shapeit_window
               #end if
             #end if
+
             #if $common.genetic_map
               --genetic-map $common.genetic_map
             #end if
+
             #if $common.ne
               --Ne $common.ne
             #end if
+
             #if $common.random_seed
               --random-seed $common.random_seed
             #end if
+
             #if $common.phase_chr
               --phase-chr $common.phase_chr
             #end if
+
             #if $common.phase_from_bp
               --phase-from-bp $common.phase_from_bp
             #end if
+
             #if $common.phase_to_bp
               --phase-to-bp $common.phase_to_bp
             #end if
-            --out $output
-            --out-format $out_format
+
+
   ]]></command>
 
   <inputs>
@@ -102,7 +113,7 @@
     <param format="vcf,vcf_bgzip" name="input" type="data" label="VCF Input"/>
 
     <param format="model" name="model_file" type="data" label="Model Input" optional="True"/>
-    <param name="model" type="select" label="Select Model" refresh_on_change="True">
+    <param name="model" type="select" label="Select Model" refresh_on_change="True" optional="True">
       <options>
         <filter type="data_meta" ref="model_file" key="models"/>
       </options>