# HG changeset patch
# User bgruening
# Date 1442584495 14400
# Node ID bb8893c72cf0ad10853a50328f95e4291c593a03
# Parent  25f127efaf7efc658bd9f51a561a31178ed992e7
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 7d50a5c7393176dcf1d25e5cc2f22544b1f6712c-dirty

diff -r 25f127efaf7e -r bb8893c72cf0 PileOMeth.xml
--- a/PileOMeth.xml	Fri Sep 18 08:03:37 2015 -0400
+++ b/PileOMeth.xml	Fri Sep 18 09:54:55 2015 -0400
@@ -34,7 +34,7 @@
                 $advanced_options.CHH
             #end if
 
-            $input_refFASTA
+            $reference_source.ref_file
             $input_sortedAlignBAM
 
             #if $main_task.task == "mbias":
@@ -42,7 +42,22 @@
             #end if
     ]]></command>
     <inputs>
-        <param name="input_refFASTA" multiple="False" type="data" format="fasta" label="Reference.fasta"/>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Load reference genome from">
+                <option value="cached">Local cache</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="Reference sequence">
+                    <options from_data_table="all_fasta"/>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
+            </when>
+        </conditional>
+
         <param name="input_sortedAlignBAM" multiple="False" type="data" format="bam" label="sorted_alignments.bam"/>
         <conditional name="main_task">
             <param name="task" type="select" label="What do you want to do?" >
@@ -64,7 +79,7 @@
                 <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation"/>
                 <param name="keepDupes" type="boolean" checked="false" truevalue="--keepDupes" falsevalue=""
                     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=""
+                <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."/>
@@ -104,7 +119,8 @@
         <test>
             <param name="task" value="extract" />
             <param name="min_MAPQ" value="2" />
-            <param name="input_refFASTA" value="cg100.fa" ftype="fasta" />
+            <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="options" value="yes"/>
@@ -114,7 +130,8 @@
             <param name="task" value="mbias" />
             <param name="min_MAPQ" value="2" />
             <param name="options" value="yes"/>
-            <param name="input_refFASTA" value="cg100.fa" ftype="fasta" />
+            <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"/>
             <output name="outFileMbiasCpG" file="test_2_output.svg" ftype="svg" compare="diff"/>
         </test>
diff -r 25f127efaf7e -r bb8893c72cf0 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 18 08:03:37 2015 -0400
+++ b/tool_dependencies.xml	Fri Sep 18 09:54:55 2015 -0400
@@ -7,7 +7,7 @@
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install prefix=$INSTALL_DIR</action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                     <environment_variable name="PILEOMETH_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>