# HG changeset patch
# User iuc
# Date 1513342747 18000
# Node ID 7f71bffac051c017853c8643437068df170021ca
# Parent  7daa3fe6db2d56b7e6a0b48c25f541513bcd4274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58

diff -r 7daa3fe6db2d -r 7f71bffac051 README.rst
--- a/README.rst	Mon Aug 28 16:54:49 2017 -0400
+++ b/README.rst	Fri Dec 15 07:59:07 2017 -0500
@@ -9,22 +9,22 @@
 By default, this tool is configured to limit the memory consumption to 1G.
 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
-In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file:
+In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file::
 
-<?xml version="1.0"?>
-<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
-    </plugins>
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-    <destinations>
-        <destination id="local" runner="local">
-            <env id="TRINITY_MAX_MEMORY">1G</env>
-        </destination>
-    </destinations>
-</job_conf>
+    <?xml version="1.0"?>
+    <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+    <job_conf>
+        <plugins>
+            <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+        </plugins>
+        <handlers>
+            <handler id="main"/>
+        </handlers>
+        <destinations>
+            <destination id="local" runner="local">
+                <env id="TRINITY_MAX_MEMORY">1G</env>
+            </destination>
+        </destinations>
+    </job_conf>
 
 
diff -r 7daa3fe6db2d -r 7f71bffac051 macros.xml
--- a/macros.xml	Mon Aug 28 16:54:49 2017 -0400
+++ b/macros.xml	Fri Dec 15 07:59:07 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>