--- a/nanopolish_methylation.xml	Tue Jun 05 18:25:34 2018 -0400
+++ b/nanopolish_methylation.xml	Wed Jun 19 03:45:24 2019 -0400
@@ -9,12 +9,28 @@
         
         #if $input_reads_raw.extension == 'fast5':
             mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
-        #else
+
+        #else if $input_reads_raw.extension == 'fast5.tar':
+            ln -s '$input_reads_raw' fast5_files.tar &&
+            mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar.bz2':
+            ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
+            mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
+
+        #else:
             ln -s '$input_reads_raw' fast5_files.tar.gz &&
             mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
+
         #end if
 
-        nanopolish index -d fast5_files/ reads.fasta &&
+        nanopolish index 
+        -d fast5_files/
+        #if $adv.input_seq_summary:
+          -s '$adv.input_seq_summary'
+        #end if 
+        reads.fasta &&
+
         ln -s '$b' reads.bam &&
         ln -s '${b.metadata.bam_index}' reads.bam.bai &&
         #if $reference_source.reference_source_selector == 'history':
@@ -39,7 +55,7 @@
     <inputs>
       <!-- index inputs -->
         <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
-        <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
+        <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
 
         <!-- variants consensus inputs -->
         <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
@@ -59,6 +75,12 @@
             <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>
+
+        <section name="adv" title="Optional data inputs">
+            <!-- optional inputs -->
+            <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>       
+        </section>        
+
         <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)"/>