Mercurial > repos > dfornika > kraken2

diff kraken2.xml @ 6:6a9137c96822 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 593a4002db3f2513974809a94db514c05fa589f6-dirty
author dfornika
date Mon, 04 Mar 2019 16:57:25 -0500
parents babd549eeb44
children 7b9218c5e126
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--- a/kraken2.xml	Mon Mar 04 16:52:55 2019 -0500
+++ b/kraken2.xml	Mon Mar 04 16:57:25 2019 -0500
@@ -11,7 +11,6 @@
         <![CDATA[
         kraken2
             --threads \${GALAXY_SLOTS:-1}
-            @INPUT_DATABASE@
             #if $single_paired.single_paired_selector == 'yes'
                 #if $forward_input.is_of_type( 'fastq' ):
                     --fastq-input
@@ -36,7 +35,7 @@
                 #end if
                 '${single_paired.input_sequences}'
             #end if
-            --db '$database'
+            --db '$kraken2_database'
             > '$output'
 	]]>
     </command>
@@ -60,7 +59,7 @@
                 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
             </when>
         </conditional>
-	<param name="kmer_db" type="select">
+	<param name="kraken2_database" type="select">
 	    <options from_data_table="kraken2_databases">
 	        <validator type="no_options" message="No Kraken2 databases are available" />
             </options>