Mercurial > repos > iuc > trinity

diff macros.xml @ 17:199aa6821ca5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
author iuc
date Fri, 15 Dec 2017 07:57:50 -0500
parents e65e640e6196
children 171b827eadf2
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line diff
--- a/macros.xml	Mon Aug 28 16:53:46 2017 -0400
+++ b/macros.xml	Fri Dec 15 07:57:50 2017 -0500
@@ -9,6 +9,28 @@
 
     <token name="@WRAPPER_VERSION@">2.4.0</token>
 
+    <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
+        #if $inputs.strand.is_strand_specific:
+            --SS_lib_type $inputs.strand.library_type
+        #end if
+
+        $inputs.jaccard_clip
+    </token>
+
+    <xml name="input_paired_strand_jaccard">
+        <conditional name="strand">
+            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+            <when value="false" />
+            <when value="true">
+                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
+                    <option value="FR">Forward-Reverse</option>
+                    <option value="RF">Reverse-Forward</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="jaccard_clip" argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/>
+    </xml>
+
     <xml name="citation">
         <citations>
             <citation type="doi">10.1038/nbt.1883</citation>