diff macros.xml @ 30:ef2c525bd8cd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"

--- a/macros.xml	Wed Oct 25 08:29:45 2017 -0400
+++ b/macros.xml	Wed Nov 06 17:02:57 2019 -0500
@@ -1,9 +1,9 @@
 <macros>
-    <token name="@DEPENDENCY_VERSION@">1.1.0.46</token>
+    <token name="@DEPENDENCY_VERSION@">1.3.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
-            <requirement type="package" version="0.1.19">samtools</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
             <yield />
         </requirements>
     </xml>
@@ -43,7 +43,14 @@
             </when>
         </conditional>
     </xml>
+    <token name="@COVERAGE@">
+        --min-coverage ${coverage_options.min_coverage}
+        --skip-coverage ${coverage_options.skip_coverage}
+        --limit-coverage ${coverage_options.limit_coverage}
+    </token>
     <xml name="par_min_cov">
-        <param name="min_coverage" argument="--coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
+        <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
+        <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
+        <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
     </xml>
 </macros>