# HG changeset patch
# User bgruening
# Date 1486987799 18000
# Node ID cda51d96a9bcb8e87632b03a6ba67f7fa1311547
# Parent  d1b66015effd14c9be73074d442c0a4c12df979f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit bff5ba839e2cb63792b0d25018460d76eb398002

diff -r d1b66015effd -r cda51d96a9bc PileOMeth.xml
--- a/PileOMeth.xml	Wed Sep 21 13:37:19 2016 -0400
+++ b/PileOMeth.xml	Mon Feb 13 07:09:59 2017 -0500
@@ -37,6 +37,9 @@
                 #if str($main_task.CTOB).strip() != "":
                     --CTOB $main_task.CTOB
                 #end if
+                $main_task.keepSingleton
+                $main_task.keepDiscordant
+                $main_task.fraction
             #end if
 
             #if $advanced_options.options=="yes":
@@ -60,6 +63,8 @@
             $input_sortedAlignBAM
 
             #if $main_task.task == "mbias":
+                $main_task.keepSingleton_mbias
+                $main_task.keepDiscordant_mbias
                 out_mbias &&
                 touch out_mbias_OT.svg &&
                 touch out_mbias_OB.svg &&
@@ -108,8 +113,15 @@
                 <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" />
                 <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
                 <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
+                <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" />
+                <param name="keepDiscordant" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" />
+                <param name="fraction" type="boolean" checked="false" truevalue="--fraction" falsevalue="" />
+                
             </when>
-            <when value="mbias"/>
+            <when value="mbias">
+                <param name="keepSingleton_mbias" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" />
+                <param name="keepDiscordant_mbias" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" />
+            </when>
         </conditional>
         <conditional name="advanced_options">
             <param name="options" type="select" label="Advanced options">
@@ -145,13 +157,13 @@
                 label="${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 +202,19 @@
             <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 d1b66015effd -r cda51d96a9bc test-data/test_2.bedGraph
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_2.bedGraph	Mon Feb 13 07:09:59 2017 -0500
@@ -0,0 +1,1 @@
+track type="bedGraph" description="output CHH methylation levels"