# HG changeset patch
# User bgruening
# Date 1442590655 14400
# Node ID e17c14e3307535960b14337ac3096df4799681dc
# Parent  f6beeefdba255a69b4cc2e50bd6db81b4d06fda8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 033c712216994524fdd120b771052ac4ca9e51c0-dirty

diff -r f6beeefdba25 -r e17c14e33075 PileOMeth.xml
--- a/PileOMeth.xml	Fri Sep 18 10:39:46 2015 -0400
+++ b/PileOMeth.xml	Fri Sep 18 11:37:35 2015 -0400
@@ -29,8 +29,8 @@
                 #end if
                 $advanced_options.keepDupes
                 $advanced_options.keepSingleton
-                -q $advanced_options.min_MAPQ
-                -p $advanced_options.min_Phred
+                -q $advanced_options.min_mapq
+                -p $advanced_options.min_phred
                 -D $advanced_options.max_pbdepth
                 $advanced_options.CHG
                 $advanced_options.CHH
@@ -69,7 +69,7 @@
             </param>
             <when value="extract">
                 <param name="mergeContext" type="boolean" checked="false" truevalue="--mergeContext" falsevalue=""
-                label="Merge per-Cytosine metrics from CpG and CHG contexts into per-CPG or per-CHG metrics" />
+                label="Merge per-Cytosine metrics from CpG and CHG contexts into per-CPG or per-CHG metrics" help="(--mergeContext)" />
             </when>
             <when value="mbias"/>
         </conditional>
@@ -84,8 +84,8 @@
                     label="By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated" />
                 <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue=""
                     label="By default, if only one read in a pair aligns (a singleton) then it's ignored." />
-                <param name="min_MAPQ" type="integer" value="10" label="Minimum MAPQ threshold to include an alignment (default 10)"/>
-                <param name="min_Phred" type="integer" value="5" label="Minimum Phred threshold to include a base (default 5). This must be >0."/>
+                <param name="min_mapq" type="integer" value="10" label="Minimum MAPQ threshold to include an alignment (default 10)"/>
+                <param name="min_phred" type="integer" value="5" label="Minimum Phred threshold to include a base (default 5). This must be >0."/>
                 <param name="max_pbdepth" type="integer" value="2000" label="Maximum per-base depth (default 2000)"/>
 
                 <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue=""
@@ -121,17 +121,17 @@
     <tests>
         <test>
             <param name="task" value="extract" />
-            <param name="min_MAPQ" value="2" />
+            <param name="min_mapq" value="2" />
             <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=""/>
+            <param name="mergeContext" value="false"/>
             <param name="options" value="yes"/>
             <output name="outFileExtractCpG" file="test_1.bedGraph" ftype="bedgraph" compare="diff"/>
         </test>
         <test>
             <param name="task" value="mbias" />
-            <param name="min_MAPQ" value="2" />
+            <param name="min_mapq" value="2" />
             <param name="options" value="yes"/>
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="cg100.fa" ftype="fasta" />