Mercurial > repos > iuc > bcftools_call

changeset 3:5337db17a5f7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6
author iuc
date Mon, 03 Oct 2016 12:19:38 -0400
parents 99dff9c8b2f3
children 6d2a5f0859cf
files bcftools_call.xml macros.xml
diffstat 2 files changed, 5 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/bcftools_call.xml	Wed Jul 13 10:55:59 2016 -0400
+++ b/bcftools_call.xml	Mon Oct 03 12:19:38 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>SNP/indel variant calling from VCF/BCF</description>
     <macros>
         <token name="@EXECUTABLE@">call</token>
@@ -114,7 +114,7 @@
                         </when>
                         <when value="trio">
                             <expand macro="macro_targets" />
-                            <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
+                            <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" />
                         </when>
                     </conditional>
                     <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
@@ -128,14 +128,14 @@
                         <when value="none">
                         </when>
                         <when value="trio">
-                            <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
+                            <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" />
                         </when>
                     </conditional>
                     <expand macro="macro_targets" />
                 </when>
             </conditional>
-            <param name="pval_threshold" type="float" label="Pval Threshold" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
-            <param name="prior" type="float" label="Prior" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
+            <param name="pval_threshold" type="float" label="Pval Threshold" value="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
+            <param name="prior" type="float" label="Prior" value="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
         </section>
         <section name="sec_file_format" expanded="false" title="File format Options">
             <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
--- a/macros.xml	Wed Jul 13 10:55:59 2016 -0400
+++ b/macros.xml	Mon Oct 03 12:19:38 2016 -0400
@@ -339,7 +339,6 @@
         </when>
         <when value="targets_file">
             <expand macro="macro_targets_file">
-               <optional>true</optional>
             </expand>
         </when>
     </conditional>