# HG changeset patch
# User bgruening
# Date 1481411270 18000
# Node ID e51dba707cf1df5fe6dff934a65891318c2a05eb
# Parent  9aaa5f5ccd061446d3dcfa11b637417db710c596
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 8768e90fb32ed53bd58ffe3c5293bfdc45d0fd77

diff -r 9aaa5f5ccd06 -r e51dba707cf1 PileOMeth.xml
--- a/PileOMeth.xml	Sun Sep 18 06:07:01 2016 -0400
+++ b/PileOMeth.xml	Sat Dec 10 18:07:50 2016 -0500
@@ -145,13 +145,13 @@
                 label="${tool.name} on ${on_string} (CHG)">
                 <filter>main_task['task'] == 'extract'</filter>
                 <filter>advanced_options['options'] == "yes"</filter>
-                <filter>advanced_options['CHG'] == "--CHG"</filter>
+                <filter>advanced_options['CHG']</filter>
             </data>
             <data  name="outFileExtractCHH" format="bedgraph" from_work_dir="output_CHH.bedGraph" 
                 label="${tool.name} on ${on_string} (CHH)">
                 <filter>main_task['task']  == 'extract'</filter>
                 <filter>advanced_options['options'] == "yes"</filter>
-                <filter>advanced_options['CHH'] == "--CHH" </filter>
+                <filter>advanced_options['CHH']</filter>
             </data>
             <data  name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg"
                 label="${tool.name} on ${on_string} (methylation bias, original top strand)">
@@ -190,6 +190,19 @@
             <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
             <output name="outFileMbiasCpG" file="test_2_output.svg" ftype="svg" compare="diff"/>
         </test>
+        <test>
+            <param name="task" value="extract" />
+            <param name="min_mapq" value="2" />
+            <param name="options" value="yes"/>
+            <param name="CHH" value="True"/>
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="cg100.fa" ftype="fasta" />
+            <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
+            <param name="mergeContext" value="false"/>
+            <param name="options" value="yes"/>
+            <output name="outFileExtractCpG" file="test_1.bedGraph" ftype="bedgraph" compare="diff"/>
+            <output name="outFileExtractCHH" file="test_2.bedGraph" ftype="bedgraph" compare="diff"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r 9aaa5f5ccd06 -r e51dba707cf1 test-data/test_2.bedGraph
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_2.bedGraph	Sat Dec 10 18:07:50 2016 -0500
@@ -0,0 +1,1 @@
+track type="bedGraph" description="output CHH methylation levels"