Mercurial > repos > iuc > jbrowse

diff jbrowse.xml @ 42:6cd09d7b5f37 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
author iuc
date Sat, 06 Feb 2021 12:01:13 +0000
parents 8774b28235bb
children
line wrap: on
line diff
--- a/jbrowse.xml	Thu Dec 31 16:00:42 2020 +0000
+++ b/jbrowse.xml	Sat Feb 06 12:01:13 2021 +0000
@@ -683,7 +683,17 @@
       <param name="gencode" value="1" />
       <param name="standalone" value="data" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
+      <output name="output">
+          <assert_contents>
+              <has_text text="&lt;gencode&gt;1&lt;/gencode&gt;"></has_text>
+              <has_text text="genome path="></has_text>
+              <has_text text="dataset id="></has_text>
+              <has_text text="history id="></has_text>
+              <has_text text="metadata"></has_text>
+              <has_text text="tool_id"></has_text>
+
+          </assert_contents>
+      </output>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -691,7 +701,16 @@
       <param name="gencode" value="11" />
       <param name="standalone" value="data" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test.xml" lines_diff="16"/>
+      <output name="output">
+        <assert_contents>
+            <has_text text="&lt;gencode&gt;11&lt;/gencode&gt;"></has_text>
+            <has_text text="genome path="></has_text>
+            <has_text text="dataset id="></has_text>
+            <has_text text="history id="></has_text>
+            <has_text text="metadata"></has_text>
+            <has_text text="tool_id"></has_text>
+        </assert_contents>
+    </output>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -708,7 +727,19 @@
         </repeat>
       </repeat>
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="bed/test.xml" lines_diff="32"/>
+      <output name="output">
+        <assert_contents>
+            <has_text text="&lt;gencode&gt;11&lt;/gencode&gt;"></has_text>
+            <has_text text="genome path="></has_text>
+            <has_text text="dataset id="></has_text>
+            <has_text text="history id="></has_text>
+            <has_text text="metadata"></has_text>
+            <has_text text="tool_id"></has_text>
+            <has_text text="trackFile path="></has_text>
+            <has_text text="ext=&quot;bed&quot; label=&quot;test-3.bed&quot;"></has_text>
+            <has_text text="NeatHTMLFeatures"></has_text>
+        </assert_contents>
+      </output>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -904,7 +935,18 @@
       </repeat>
 
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gff3/test.xml" lines_diff="260" />
+      <output name="output">
+          <assert_contents>
+                <has_text text="Auto Coloured"/>
+                <has_text text="A.gff"/>
+                <has_text text="B.gff"/>
+                <has_text text="C.gff"/>
+                <has_text text="D.gff"/>
+                <has_text text="Scaled Colour"/>
+                <has_text text="1.gff"/>
+                <has_text text="2.gff"/>
+          </assert_contents>
+      </output>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -967,7 +1009,14 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="menus/test.xml" lines_diff="44"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="With menu or index"/>
+                <has_text text="Some menu item"/>
+                <has_text text="Frame title"/>
+                <has_text text="dijitIconNewTask"/>
+            </assert_contents>
+        </output>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -1005,7 +1054,13 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="track_config/test.xml" lines_diff="30"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="With canvas config"></has_text>
+                <has_text text="&lt;transcriptType&gt;transcript&lt;/transcriptType&gt;"></has_text>
+                <has_text text="&lt;subParts&gt;exon&lt;/subParts&gt;"></has_text>
+            </assert_contents>
+        </output>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -1057,7 +1112,15 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="custom_config/test.xml" lines_diff="30"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="1.gff"/>
+                <has_text text="collapsed"/>
+                <has_text text="150"/>
+                <has_text text="maxFeatureScreenDensity"/>
+                <has_text text="style.strandArrow"/>
+            </assert_contents>
+        </output>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -1076,7 +1139,13 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="bam/test.xml" lines_diff="42"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="merlin-sample.bam"/>
+                <has_text text="sort_order=&quot;coordinate&quot;"/>
+                <has_text text="bam_index"/>
+            </assert_contents>
+        </output>
     </test>
 
     <test>
@@ -1086,7 +1155,11 @@
         <param name="gencode" value="1" />
         <param name="standalone" value="data" />
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
+        <output name="output">
+            <assert_contents>
+                <has_text text="merlin.fa"/>
+            </assert_contents>
+        </output>
     </test>
 
     <test>
@@ -1133,7 +1206,11 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="endpoints/test.xml" lines_diff="16"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="http://example.org.external/sparql/"/>
+            </assert_contents>
+        </output>
     </test>
   </tests>
   <help><![CDATA[