Mercurial > repos > iuc > bcftools_stats

diff bcftools_stats.xml @ 4:e37d2899945c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
author iuc
date Sat, 11 Mar 2017 17:56:32 -0500
parents 1bef9d3b2db7
children 64db9662b6b3
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--- a/bcftools_stats.xml	Tue Jan 31 12:40:37 2017 -0500
+++ b/bcftools_stats.xml	Sat Mar 11 17:56:32 2017 -0500
@@ -1,11 +1,13 @@
 <?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@">
     <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
     <macros>
         <token name="@EXECUTABLE@">stats</token>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="1.3.1">samtools</requirement>
+    </expand>
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
 @PREPARE_ENV@
@@ -80,7 +82,7 @@
                     <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
                 </when>
             </conditional>
-            <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="Reference sequence" />
+            <expand macro="macro_fasta_ref" />
             <expand macro="macro_exons_file" />
             <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 
                    help="Collect stats for sites with ID separately (known vs novel)" />