--- a/mash_screen.xml	Thu Jul 25 17:37:23 2019 -0400
+++ b/mash_screen.xml	Thu Feb 13 19:34:55 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0">
+<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy1" profile="19.01">
     <description>determines how well query sequences are contained within a pool of sequences.</description>
     <macros>
         <import>macros.xml</import>
@@ -8,14 +8,13 @@
     </requirements>
     <version_command>mash --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '${queries.fields.path}/sketch.msh' queries.msh &&
+        ln -s '$queries' queries.msh &&
         mash screen
-             -p \${GALAXY_SLOTS:-1}  
              $winner_takes_all
              -i $minimum_identity_to_report
              -v $maximum_p_value_to_report
              queries.msh
-	     #if str( $pool_input.pool_input_selector ) == "paired"
+             #if str( $pool_input.pool_input_selector ) == "paired"
                '$pool_input.pool_1' '$pool_input.pool_2'
              #end if
              #if str( $pool_input.pool_input_selector ) == "paired_collection"
@@ -27,7 +26,7 @@
              > '$output'
     ]]></command>
     <inputs>
-	<conditional name="pool_input">
+        <conditional name="pool_input">
             <param name="pool_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
                 <option value="paired">Paired</option>
                 <option value="single">Single</option>
@@ -44,11 +43,7 @@
                 <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="select">
-            <options from_data_table="mash_sketches">
-                <validator type="no_options" message="No mash sketches are available." />
-            </options>
-        </param>
+        <param name="queries" type="data" format="msh" />
         <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."/>
@@ -59,32 +54,21 @@
     <tests>
         <test>
             <param name="queries" value="NZ_MYON01000010.1.msh"/>
-	    <param name="pool_input_selector" value="single"/>
+            <param name="pool_input_selector" value="single"/>
             <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
         </test>
         <test>
             <param name="queries" value="NZ_MYON01000010.1.msh"/>
-	    <param name="pool_input_selector" value="single"/>
+            <param name="pool_input_selector" value="single"/>
             <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
         </test>
         <test>
             <param name="queries" value="NZ_MYON01000010.1.msh"/>
-	    <param name="pool_input_selector" value="paired"/>
+            <param name="pool_input_selector" value="paired"/>
             <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
-	    <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
-            <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
-        </test>
-	<test>
-            <param name="queries" value="NZ_MYON01000010.1.msh"/>
-	    <param name="pool_input_selector" value="paired_collection"/>
-	    <param name="pool">
-	      <collection type="paired">
-		<element name="forward" value="ERR024951_seqtk_sample_1000_1.fastq"/>
-		<element name="reverse" value="ERR024951_seqtk_sample_1000_2.fastq"/>
-	      </collection>
-	    </param>
+            <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
         </test>
     </tests>
@@ -113,6 +97,6 @@
   year={2016},
   publisher={BioMed Central}
   }
-	</citation>
+        </citation>
     </citations>
 </tool>