Mercurial > repos > iuc > jbrowse

diff jbrowse.xml @ 19:8f33c9fbc119 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
author iuc
date Fri, 06 Jul 2018 06:10:18 -0400
parents 836d1aa3e89a
children 1c718d8b3532
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line diff
--- a/jbrowse.xml	Thu Nov 16 09:44:45 2017 -0500
+++ b/jbrowse.xml	Fri Jul 06 06:10:18 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3">
+<tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
   <description>genome browser</description>
   <macros>
     <import>macros.xml</import>
@@ -601,7 +601,7 @@
       <param name="gencode" value="1" />
       <param name="standalone" value="Data Directory" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test-1.xml" lines_diff="4" />
+      <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -805,7 +805,7 @@
       </repeat>
 
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gff3/test.xml" lines_diff="64" />
+      <output name="output" file="gff3/test.xml" lines_diff="256" />
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -908,13 +908,33 @@
         <output name="output" file="track_config/test.xml" lines_diff="26"/>
     </test>
     <test>
+        <param name="reference_genome|genome_type_select" value="history"/>
+        <param name="reference_genome|genomes" value="merlin.fa"/>
+        <param name="gencode" value="11" />
+        <param name="standalone" value="Data Directory" />
+
+        <repeat name="track_groups">
+            <param name="category" value="Auto Coloured" />
+            <repeat name="data_tracks">
+                <conditional name="data_format">
+                    <param name="data_format_select" value="pileup"/>
+                    <param name="annotation" value="bam/merlin-sample.bam"/>
+                </conditional>
+            </repeat>
+        </repeat>
+
+        <param name="uglyTestingHack" value="enabled" />
+        <output name="output" file="bam/test.xml" lines_diff="48"/>
+    </test>
+
+    <test>
         <!-- data_table -->
         <param name="reference_genome|genome_type_select" value="indexed"/>
         <param name="reference_genome|genomes" value="merlin"/>
         <param name="gencode" value="1" />
         <param name="standalone" value="Data Directory" />
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
+        <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
     </test>
   </tests>
   <help><![CDATA[