# HG changeset patch
# User simon-gladman
# Date 1465285216 14400
# Node ID f0b139f53e1fd96207bee29ea91a106ef18689b0
# Parent  8b69e4b18a5f95f50e55dff9e49af59b48a521eb
Added genbank support

diff -r 8b69e4b18a5f -r f0b139f53e1f snippy.xml
--- a/snippy.xml	Mon Jun 06 00:54:10 2016 -0400
+++ b/snippy.xml	Tue Jun 07 03:40:16 2016 -0400
@@ -13,11 +13,21 @@
     </stdio>
 
     <command><![CDATA[
-      cp $ref foo.fna &&
+      #if str( $reftype.ref_type_selector ) == "fasta"
+        cp $reftype.ref foo.fna &&
+      #end if
+      #if str( $reftype.ref_type_selector ) == "genbank"
+        cp $reftype.ref foo.gbk &&
+      #end if
       snippy
       --outdir out
       --cpus "\${GALAXY_SLOTS:-1}"
-      --ref foo.fna
+      #if str( $reftype.ref_type_selector ) == "fasta"
+        --ref foo.fna
+      #end if
+      #if str( $reftype.ref_type_selector ) == "genbank"
+        --ref foo.gbk
+      #end if
       $cleanup
       #if str( $advanced.is_advanced ) == "advanced"
         --mapqual $advanced.mapqual
@@ -52,7 +62,18 @@
 
     ]]></command>
     <inputs>
-      <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" />
+      <conditional name="reftype">
+        <param name="ref_type_selector" type="select" label="Reference type" help="File type of the reference file. (Fasta or Genbank)">
+          <option value="genbank">Genbank</option>
+          <option value="fasta">Fasta</option>
+        </param>
+        <when value="fasta">
+          <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" />
+        </when>
+        <when value="genbank">
+          <param name="ref" type="data" format="genbank" label="Reference Genbank" help="Genbank file to use as the reference" />
+        </when>
+      </conditional>
       <conditional name="fastq_input">
         <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
           <option value="paired">Paired</option>
@@ -97,7 +118,7 @@
       <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/>
       <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/>
       <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/>
-      <data format="text" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/>
+      <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/>
       <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/>
       <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
       <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
@@ -118,35 +139,58 @@
 
 
     <help><![CDATA[
-      This is a change to force a reinstall
-        Synopsis:
+Synopsis:
   snippy 3.0 - fast bacterial variant calling from NGS reads
+
 Author:
   Torsten Seemann <torsten.seemann@gmail.com>
+
 Usage:
   snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz>
+
   snippy [options] --outdir <dir> --ref <ref> --se <454.fastq>
+
   snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz>
+
 Options:
   --help            This help
+
   --version         Print version and exit
+
   --citation        Print citation for referencing snippy
+
   --quiet           No screen output (default OFF)
+
   --cpus [N]        Maximum number of CPU cores to use (default '8')
+
   --reference [X]   Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')
+
   --outdir [X]      Output folder (default '')
+
   --prefix [X]      Prefix for output files (default 'snps')
+
   --force           Force overwrite of existing output folder (default OFF)
+
   --pe1|R1|left [X] Reads, paired-end R1 (left) (default '')
+
   --pe2|R2|right [X] Reads, paired-end R2 (right) (default '')
+
   --se|single [X]   Single-end reads (default '')
+
   --peil [X]        Reads, paired-end R1/R2 interleaved (default '')
+
   --mapqual [n.n]   Minimum mapping quality to allow (default '60')
+
   --mincov [N]      Minimum coverage of variant site (default '10')
+
   --minfrac [n.n]   Minumum proportion for variant evidence (default '0.9')
+
   --report          Produce long report with visual alignment (slow) (default OFF)
+
   --cleanup         Remove all non-SNP files: BAMs, indices etc (default OFF)
+
   --rgid [X]        Use this @RG ID: in the BAM header (default '')
+
   --bwaopt [X]      Extra BWA MEM options, eg. -x pacbio (default '')
 
     ]]></help>