Mercurial > repos > dfornika > kraken2

diff kraken2.xml @ 8:d120504e741a 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 17:17:43 -0500
parents 7b9218c5e126
children a811afe91eab
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--- a/kraken2.xml	Mon Mar 04 17:07:17 2019 -0500
+++ b/kraken2.xml	Mon Mar 04 17:17:43 2019 -0500
@@ -9,6 +9,7 @@
     <version_command>kraken2 --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
+        @SET_DATABASE_PATH@
         kraken2
             --threads \${GALAXY_SLOTS:-1}
 	    --db '$kraken2_database'
@@ -35,7 +36,6 @@
             <when value="yes">
                 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
                 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
-                <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
             </when>
             <when value="no">
                 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>