Mercurial > repos > iuc > trinity_samples_qccheck

diff macros.xml @ 19:1b1a25f93f80 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:49:25 +0000
parents b58468eb4e64
children
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--- a/macros.xml	Sun Dec 19 16:19:58 2021 +0000
+++ b/macros.xml	Tue Apr 11 19:49:25 2023 +0000
@@ -1,8 +1,7 @@
-<?xml version="1.0"?>
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">trinity</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">trinity</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -11,10 +10,11 @@
             <xref type="bio.tools">trinity</xref>
         </xrefs>
     </xml>
-    <token name="@WRAPPER_VERSION@">2.9.1</token>
+    <token name="@TOOL_VERSION@">2.15.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
-        #if $pool.inputs.strand.is_strand_specific:
+        #if $pool.inputs.strand.is_strand_specific == 'true':
             --SS_lib_type $pool.inputs.strand.library_type
         #end if
 
@@ -23,7 +23,10 @@
 
     <xml name="input_paired_strand_jaccard">
         <conditional name="strand">
-            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+            <param name="is_strand_specific" type="select" label="Strand specific data">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
             <when value="false" />
             <when value="true">
                 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
@@ -35,6 +38,22 @@
         <param 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="is_strand_specific_f_r">
+        <conditional name="strand">
+            <param name="is_strand_specific" type="select" label="Strand specific data">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false"/>
+            <when value="true">
+                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
+                    <option value="F">F</option>
+                    <option value="R">R</option>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+
     <xml name="citation">
         <citations>
             <citation type="doi">10.1038/nbt.1883</citation>