# HG changeset patch
# User dfornika
# Date 1564083110 14400
# Node ID cf0d6a872bd45de640f4f06282ef094fd370fe12
# Parent  948dba53a39111712d4b737bb4678f0f5dc12189
planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/mash commit 423cf96266f6ac433052ff72edb1397502313010-dirty

diff -r 948dba53a391 -r cf0d6a872bd4 mash_dist.xml
--- a/mash_dist.xml	Tue Jan 29 14:58:37 2019 -0500
+++ b/mash_dist.xml	Thu Jul 25 15:31:50 2019 -0400
@@ -31,7 +31,11 @@
              > '$output'
     ]]></command>
     <inputs>
-        <param name="reference" type="data" format="@INTYPES@,binary" />
+        <param name="reference" type="select">
+            <options from_data_table="mash_sketches">
+                <validator type="no_options" message="No Mash sketches are available." />
+            </options>
+        </param>
         <conditional name="query_input">
             <param name="query_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
                 <option value="paired">Paired</option>
@@ -46,7 +50,7 @@
             <when value="single">
                 <param name="query" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
             </when>
-	    <when value="collection">
+            <when value="collection">
                 <param name="query" format="@INTYPES@" type="data_collection" collection_type="list" label="Select a collection" help="See help section for an explanation of dataset collections"/>
             </when>
             <when value="paired_collection">
diff -r 948dba53a391 -r cf0d6a872bd4 mash_screen.xml
--- a/mash_screen.xml	Tue Jan 29 14:58:37 2019 -0500
+++ b/mash_screen.xml	Thu Jul 25 15:31:50 2019 -0400
@@ -8,7 +8,7 @@
     </requirements>
     <version_command>mash --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$queries' queries.msh &&
+        ln -s '${queries}/sketch.msh' queries.msh &&
         mash screen
              $winner_takes_all
              -i $minimum_identity_to_report
@@ -43,7 +43,11 @@
                 <param name="pool" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
             </when>
         </conditional>
-        <param name="queries" type="data" format="binary" />
+	<param name="queries" type="select">
+            <options from_data_table="mash_sketches">
+                <validator type="no_options" message="No mash sketches are available." />
+            </options>
+        </param>
         <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/>
         <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." />
         <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/>