# HG changeset patch
# User iuc
# Date 1513342866 18000
# Node ID 8c4ec8bbe5aca5945881e4cc63f1c8a43ed54151
# Parent  b99f4e46129199244d3d981a63cc4baee501f0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58

diff -r b99f4e461291 -r 8c4ec8bbe5ac README.rst
--- a/README.rst	Mon Aug 28 16:55:25 2017 -0400
+++ b/README.rst	Fri Dec 15 08:01:06 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 b99f4e461291 -r 8c4ec8bbe5ac macros.xml
--- a/macros.xml	Mon Aug 28 16:55:25 2017 -0400
+++ b/macros.xml	Fri Dec 15 08:01:06 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>