# HG changeset patch
# User iuc
# Date 1548277147 18000
# Node ID 4f453db80800f6858831702cb06f50ec9d8cbcb6
# Parent  867692ec85aae935a36d51faae1a3177b3dac7c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 91435d801528addac840722e9a0092b2d342b8bb

diff -r 867692ec85aa -r 4f453db80800 mash_screen.xml
--- a/mash_screen.xml	Mon Jan 07 15:09:31 2019 -0500
+++ b/mash_screen.xml	Wed Jan 23 15:59:07 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0" profile="19.01">
+<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>
@@ -14,12 +14,36 @@
              -i $minimum_identity_to_report
              -v $maximum_p_value_to_report
              queries.msh
-             '${ str($pool).replace(',', '\' \'') }'
+             #if str( $pool_input.pool_input_selector ) == "paired"
+               '$pool_input.pool_1' '$pool_input.pool_2'
+             #end if
+             #if str( $pool_input.pool_input_selector ) == "paired_collection"
+               '$pool_input.pool.forward' '$pool_input.pool.reverse'
+             #end if
+             #if str( $pool_input.pool_input_selector ) == "single"
+               '$pool_input.pool'
+             #end if
              > '$output'
     ]]></command>
     <inputs>
+        <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>
+                <option value="paired_collection">Paired Collection</option>
+            </param>
+            <when value="paired">
+                <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
+                <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+            </when>
+            <when value="single">
+                <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
+            </when>
+            <when value="paired_collection">
+                <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="msh" />
-        <param type="data" multiple="true" name="pool" format="@INTYPES@" />
         <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."/>
@@ -30,17 +54,21 @@
     <tests>
         <test>
             <param name="queries" value="NZ_MYON01000010.1.msh"/>
+            <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" 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" value="ERR024951_seqtk_sample_1000_1.fastq,ERR024951_seqtk_sample_1000_2.fastq"/>
+            <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>
     </tests>
@@ -69,6 +97,6 @@
   year={2016},
   publisher={BioMed Central}
   }
-	</citation>
+        </citation>
     </citations>
 </tool>