Mercurial > repos > dfornika > kraken2

changeset 1:7932d09da19b 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 14:47:57 -0500
parents a77e88d426d9
children f8683d234222
files kraken2.xml macros.xml
diffstat 2 files changed, 0 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/kraken2.xml	Fri Mar 01 12:43:26 2019 -0500
+++ b/kraken2.xml	Mon Mar 04 14:47:57 2019 -0500
@@ -9,12 +9,9 @@
     <version_command>kraken2 --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
-        @SET_DATABASE_PATH@ &&
-
         kraken2
             --threads \${GALAXY_SLOTS:-1}
             @INPUT_DATABASE@
-
             #if $single_paired.single_paired_selector == 'yes'
                 #if $forward_input.is_of_type( 'fastq' ):
                     --fastq-input
@@ -63,7 +60,6 @@
                 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
             </when>
         </conditional>
-        <param name="" type="" format="" />
     </inputs>
     <outputs>
         <data name="output" format="" />
--- a/macros.xml	Fri Mar 01 12:43:26 2019 -0500
+++ b/macros.xml	Mon Mar 04 14:47:57 2019 -0500
@@ -10,6 +10,4 @@
             </options>
         </param>
     </xml>
-    <token name="@SET_DATABASE_PATH@">if [ -d '${kraken2_database.fields.path}/${kraken2_database.fields.name}' ]; then export KRAKEN2_DEFAULT_DB='${kraken2_database.fields.path}/${kraken2_database.fields.name}'; else export KRAKEN2_DEFAULT_DB='${kraken_database.fields.path}'; fi</token>
-    <token name="@INPUT_DATABASE@">--db "\$KRAKEN2_DEFAULT_DB"</token>
 </macros>