Mercurial > repos > mvdbeek > tepid_discover

changeset 5:afe2a09f802b draft default tip

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planemo upload for repository https://github.com/ListerLab/TEPID commit 48d24b91382cfbe7749d131657efbad47a28f569-dirty
author mvdbeek
date Fri, 06 Jan 2017 08:36:08 -0500
parents df634cd04be7
children
files tepid-discover.xml
diffstat 1 files changed, 20 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/tepid-discover.xml	Fri Jan 06 08:23:13 2017 -0500
+++ b/tepid-discover.xml	Fri Jan 06 08:36:08 2017 -0500
@@ -52,16 +52,16 @@
     </inputs>
     <outputs>
         <data name="insertions_out" format="bed" label="tepid_discover insertions on ${on_string}">
-            <filter>not insertions</filter>
+            <filter>not deletions</filter>
         </data>
         <data name="insertion_reads_out" format="txt" label="tepid_discover reads supporting insertions for ${on_string}">
-            <filter>not insertions"</filter>
+            <filter>not deletions</filter>
         </data>
         <data name="deletions_out" format="bed" label="tepid_discover deletions on ${on_string}">
-            <filter>not deletions</filter>
+            <filter>not insertions</filter>
         </data>
         <data name="deletion_reads_out" format="txt" label="tepid_discover reads supporting deletions for ${on_string}">
-            <filter>not deletions</filter>
+            <filter>not insertions"</filter>
         </data>
     </outputs>
     <tests>
@@ -74,6 +74,22 @@
             <output name="insertion_reads_out" file="insertion_reads_test.txt"/>
             <output name="deletion_reads_out" file="deletion_reads_test.txt"/>
         </test>
+        <test>
+            <param name="bowtie2_bam" value="conc.bam"/>
+            <param name="split_bam" value="split.bam"/>
+            <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/>
+            <param name="deletions" value="true"/>
+            <output name="deletions_out" file="deletions_test.bed"/>
+            <output name="deletion_reads_out" file="deletion_reads_test.txt"/>
+        </test>
+        <test>
+            <param name="bowtie2_bam" value="conc.bam"/>
+            <param name="split_bam" value="split.bam"/>
+            <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/>
+            <param name="insertions" value="true"/>
+            <output name="insertions_out" file="insertions_test.bed"/>
+            <output name="insertion_reads_out" file="insertion_reads_test.txt"/>
+        </test>
     </tests>
     <help><![CDATA[
 TEPID -- transposable element polymorphism identification