# HG changeset patch
# User nml
# Date 1548945544 18000
# Node ID b02c775b27c84e8ef8695bebff2e9d21ebac83a3
# Parent  b60c187a3a0240998246a5d78ce0dc0e0d150e34
planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23

diff -r b60c187a3a02 -r b02c775b27c8 ectyper.xml
--- a/ectyper.xml	Thu Jan 03 15:21:29 2019 -0500
+++ b/ectyper.xml	Thu Jan 31 09:39:04 2019 -0500
@@ -19,6 +19,10 @@
     ln -s "${input}" "${input.name}" &&
     #set $genomes = $input.name
   #end if
+
+  #if $mash_input
+    ln -s "${mash_input}" mash_sketch.msh &&
+  #end if
  
   ectyper  --cores \${GALAXY_SLOTS:-4} 
   --input "${genomes}" 
@@ -27,6 +31,9 @@
   #if $adv_param.verifyEcoli
     --verify
   #end if
+  #if $mash_input
+    --refseq mash_sketch.msh
+  #end if   
   #if $adv_param.alleleSequence
     --sequence
   #end if
@@ -34,7 +41,8 @@
   ]]>
   </command>
   <inputs>
-    <param name="input" type="data"  format="fastq,fasta" label="Input(s)" help="FASTA or FASTQ file(s) with contig(s)"/>
+    <param name="input" type="data"  format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s) with contig(s)"/>
+    <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide MASH sketches to find closest genome (in case O/H typing fails)"/>
     <section name="adv_param" title="Advanced parameters" expanded="False">
       <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/>
       <param name="percentLength" type="integer" value="50" min="1" max="100"/>
@@ -75,8 +83,9 @@
 
 **Input:**
 
-Accepts a variety of inputs including single or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results draft assemblies are recommended.
+Accepts a variety of inputs including single or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results draft assemblies are recommended. 
 
+Optionally select a MASH RefSeq genome sketch (version 2.0 and above) for cases when O/H typing would fail. Download RefSeq genome sketch containing 91,283 genomes with 1000 hashes each directly from https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh . 
 
 **Output:**
 
@@ -101,4 +110,4 @@
   url = {https://github.com/phac-nml/ecoli_serotyping}
     }</citation>
 </citations>
-</tool>
+</tool>
\ No newline at end of file