# HG changeset patch
# User dfornika
# Date 1551737237 18000
# Node ID 7b9218c5e126a8659e80dea36a400ad69d61d194
# Parent  6a9137c96822213c56c6049935307f7288971955
planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 593a4002db3f2513974809a94db514c05fa589f6-dirty

diff -r 6a9137c96822 -r 7b9218c5e126 kraken2.xml
--- a/kraken2.xml	Mon Mar 04 16:57:25 2019 -0500
+++ b/kraken2.xml	Mon Mar 04 17:07:17 2019 -0500
@@ -11,31 +11,14 @@
         <![CDATA[
         kraken2
             --threads \${GALAXY_SLOTS:-1}
+	    --db '$kraken2_database'
             #if $single_paired.single_paired_selector == 'yes'
-                #if $forward_input.is_of_type( 'fastq' ):
-                    --fastq-input
-                #else:
-                    --fasta-input
-                #end if
                 '${single_paired.forward_input}' '${single_paired.reverse_input}'
-                ${single_paired.check_names}
             #elif $single_paired.single_paired_selector == "collection":
-                #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
-                    --fastq-input
-                #else:
-                    --fasta-input
-                #end if
                 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
-                ${single_paired.check_names}
             #else:
-                #if $single_paired.input_sequences.is_of_type('fastq')
-                    --fastq-input
-                #else:
-                    --fasta-input
-                #end if
                 '${single_paired.input_sequences}'
             #end if
-            --db '$kraken2_database'
             > '$output'
 	]]>
     </command>
@@ -48,7 +31,6 @@
             </param>
             <when value="collection">
                 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
-                <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
             </when>
             <when value="yes">
                 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>