# HG changeset patch
# User iuc
# Date 1475511680 14400
# Node ID cd84903d45c1d234cd7d29216139939ad62f225a
# Parent  ef99a1afcb66c0690a2d796b5ed8f534a38ada97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6

diff -r ef99a1afcb66 -r cd84903d45c1 bcftools_cnv.xml
--- a/bcftools_cnv.xml	Wed Jul 13 10:56:09 2016 -0400
+++ b/bcftools_cnv.xml	Mon Oct 03 12:21:20 2016 -0400
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
     <description>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description>
     <macros>
         <token name="@EXECUTABLE@">cnv</token>
@@ -99,7 +99,7 @@
         </section>
         <section name="sec_hmm" expanded="false" title="HMM Options">
             <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" />
-            <param name="optimize" type="float" value="" imin="0." max="1." label="Optimize" optional="True" >
+            <param name="optimize" type="float" value="" min="0." max="1." label="Optimize" optional="True" >
                 <help>
                   Iteratively estimate the fraction of aberrant cells, down to the given fraction. 
                   Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise.
@@ -111,7 +111,7 @@
                     Setting to 0 calls both independently, setting to 1 forces the same copy number state in both.
                 </help>
             </param>
-            <param name="xy_prob" type="float" value="" min="0." max="1." label="Xy Prob" default="1e-9" optional="True">
+            <param name="xy_prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9" optional="True">
                 <help>
                     The HMM probability of transition to another copy number state. 
                     Increasing this value leads to smaller and more frequent calls. 
@@ -129,7 +129,7 @@
             <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true" 
                    help="Expected BAF deviation in control, defaults to: 0.04" />
 
-            <param name="LRR_weight" type="float" default="" label="LRR Weight" optional="True" >
+            <param name="LRR_weight" type="float" label="LRR Weight" optional="True" >
                 <help>
                     Relative contribution from LRR.  
                     With noisy data, this option can have big effect on the number of calls produced. 
@@ -141,7 +141,7 @@
                    help="Expected LRR deviation in query, default is: 0.2" />
             <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation" 
                    help="Expected LRR deviation in control, default is: 0.2" />
-            <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" default="10" optional="True" 
+            <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" value="10" optional="True" 
                    help="Window of LRR moving average smoothing" />
 
         </section>
diff -r ef99a1afcb66 -r cd84903d45c1 macros.xml
--- a/macros.xml	Wed Jul 13 10:56:09 2016 -0400
+++ b/macros.xml	Mon Oct 03 12:21:20 2016 -0400
@@ -339,7 +339,6 @@
         </when>
         <when value="targets_file">
             <expand macro="macro_targets_file">
-               <optional>true</optional>
             </expand>
         </when>
     </conditional>