Mercurial > repos > devteam > samtools_rmdup

changeset 5:586f9e1cdb2b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:45:55 -0400
parents 9129584416e2
children
files macros.xml
diffstat 1 files changed, 15 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue May 09 11:18:58 2017 -0400
+++ b/macros.xml	Mon Jul 29 08:45:55 2019 -0400
@@ -6,6 +6,21 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">1.3.1</token>
+    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
+    <xml name="filter_options">
+        <option value="1">Read is paired</option>
+        <option value="2">Read is mapped in a proper pair</option>
+        <option value="4">The read is unmapped</option>
+        <option value="8">The mate is unmapped</option>
+        <option value="16">Read strand</option>
+        <option value="32">Mate strand</option>
+        <option value="48">Read is the first in a pair</option>
+        <option value="64">Read is the second in a pair</option>
+        <option value="256">The alignment or this read is not primary</option>
+        <option value="512">The read fails platform/vendor quality checks</option>
+        <option value="768">The read is a PCR or optical duplicate</option>
+        <option value="1024">Supplementary alignment</option>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="bibtex">