# HG changeset patch
# User iuc
# Date 1485884071 18000
# Node ID 3e85f6c5cf8eebb7591bcdef5e2717b1f84bf92e
# Parent  a4f3b1dbb34520ff582ab71ef7fceaaddd36b8ea
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e

diff -r a4f3b1dbb345 -r 3e85f6c5cf8e bcftools_call.xml
--- a/bcftools_call.xml	Sat Jan 21 06:51:16 2017 -0500
+++ b/bcftools_call.xml	Tue Jan 31 12:34:31 2017 -0500
@@ -1,9 +1,32 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.2">
     <description>SNP/indel variant calling from VCF/BCF</description>
     <macros>
         <token name="@EXECUTABLE@">call</token>
         <import>macros.xml</import>
+        <xml name="macro_novel_rate">
+            <param name="novel_rate_snp" type="float" label="Novel Rate SNP" value="" optional="true" 
+                   help="likelihood of novel mutation for constrained trio calling, see man page for details" />
+            <param name="novel_rate_del" type="float" label="Novel Rate Deletions" value="" optional="true" 
+                   help="likelihood of novel mutation for constrained trio calling, see man page for details" />
+            <param name="novel_rate_ins" type="float" label="Novel Rate Insertions" value="" optional="true" 
+                   help="likelihood of novel mutation for constrained trio calling, see man page for details" />
+        </xml>
+        <token name="@NOVEL_RATE@">
+            #set $novel_rate = []
+            #if str($section.genotypes.novel_rate_snp):
+              #silent $novel_rate.append(str($section.genotypes.novel_rate_snp))
+            #end if
+            #if str($section.genotypes.novel_rate_del):
+              #silent $novel_rate.append(str($section.genotypes.novel_rate_del))
+            #end if
+            #if str($section.genotypes.novel_rate_ins):
+              #silent $novel_rate.append(str($section.genotypes.novel_rate_ins))
+            #end if
+            #if len($novel_rate) > 0:
+               --novel-rate '#echo ','.join($novel_rate)#'
+            #end if
+        </token>
     </macros>
     <expand macro="requirements" />
     <expand macro="version_command" />
@@ -34,9 +57,7 @@
  #else
    #if $section.genotypes.constrain == 'trio':
     --constrain trio
-    #if $section.genotypes.novel_rate:
-     --novel-rate '$section.genotypes.novel_rate'
-    #end if
+    @NOVEL_RATE@
    #end if
    #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
    @TARGETS@
@@ -114,7 +135,7 @@
                         </when>
                         <when value="trio">
                             <expand macro="macro_targets" />
-                            <param name="novel_rate" type="float" label="Novel Rate" value="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
+                            <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
                     <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
@@ -128,7 +149,7 @@
                         <when value="none">
                         </when>
                         <when value="trio">
-                            <param name="novel_rate" type="float" label="Novel Rate" value="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
+                            <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
                     <expand macro="macro_targets" />
@@ -227,6 +248,8 @@
   - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. 
   - The original calling model can be invoked with the -c option.
 
+The novel-rate option can be set to modify the likelihood of novel mutation for constrained -C trio calling. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is given, the same mutation rate Pn is used for SNPs and indels. 
+
 @REGIONS_HELP@
 @TARGETS_HELP@
 
diff -r a4f3b1dbb345 -r 3e85f6c5cf8e macros.xml
--- a/macros.xml	Sat Jan 21 06:51:16 2017 -0500
+++ b/macros.xml	Tue Jan 31 12:34:31 2017 -0500
@@ -14,7 +14,9 @@
       <requirement type="package" version="1.3">bcftools</requirement>
       <!-- conda dependency -->
       <requirement type="package" version="1.3">htslib</requirement>
+      <!-- htslib provides tabix and bgzip
       <requirement type="package" version="0.2.6">tabix</requirement>
+      -->
       <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
   </xml>