--- a/nanopolish_methylation.xml	Wed May 30 11:55:55 2018 -0400
+++ b/nanopolish_methylation.xml	Tue Jun 05 17:56:11 2018 -0400
@@ -17,12 +17,20 @@
         nanopolish index -d fast5_files/ reads.fasta &&
         ln -s '$b' reads.bam &&
         ln -s '${b.metadata.bam_index}' reads.bam.bai &&
-        ln -s '$g' genome.fa &&
+        #if $reference_source.reference_source_selector == 'history':
+            ln -f -s '$reference_source.ref_file' genome.fa &&
+        #else:
+            ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
+        #end if
         
         nanopolish call-methylation
         -r reads.fasta
         -b reads.bam
         -g genome.fa
+        #if str($batchsize):
+            -K $batchsize
+        #end if
+        --threads "\${GALAXY_SLOTS:-4}"        
         #if $w and str($w).strip():
           -w "${w}"
         #end if  
@@ -35,10 +43,25 @@
 
         <!-- variants consensus inputs -->
         <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
-        <param type="data" argument="-g" format="fasta" label="The reference genome"/>
-
+        <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">
+              </options>
+              <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 following 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 argument="-w" type="text" optional="true"
             label="find variants in window of region chromsome:start-end" />
+        <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/>
 
     </inputs>
 
@@ -48,18 +71,26 @@
     </outputs>
     <tests>
         <test>
-      <!-- index test -->
             <param name="input_merged" ftype="fasta" value="reads.fasta" />
             <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
-            
-      <!-- variants consensus test -->
             <param name="b" value="reads.sorted.bam" />
-            <param name="g" value="draft.fa" />
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="draft.fa" />
             <param name="w" value="tig00000001:200000-202000" />
-            
+            <param name="batchsize" value="512" />
             <output name="output_methylation_calls" file="methylation_calls.tsv" />
         </test>
-    </tests>
+         <test>
+            <param name="input_merged" ftype="fasta" value="reads.fasta" />
+            <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
+            <param name="reference_source_selector" value="cached" />
+            <param name="ref_file" value="draft"/>
+            <param name="b" value="reads.sorted.bam" />
+            <param name="w" value="tig00000001:200000-202000" />
+            <param name="batchsize" value="512" />
+            <output name="output_methylation_calls" file="methylation_calls.tsv" />
+        </test>
+    </tests>    
     <help><![CDATA[
         Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
         Classify nucleotides as methylated or not.