# HG changeset patch
# User pimarin
# Date 1649253168 0
# Node ID b135c5908e8c8d75ef13f83e1f252d45d6ce3afb
# Parent  856d50c93de98add92dea7cefd3e2e0b2b8dc4a9
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"

diff -r 856d50c93de9 -r b135c5908e8c macro.xml
--- a/macro.xml	Wed Apr 06 10:34:16 2022 +0000
+++ b/macro.xml	Wed Apr 06 13:52:48 2022 +0000
@@ -2,7 +2,7 @@
 <macros>
   <token name="@TOOL_VERSION@">1.8.1</token>
   <token name="@VERSION_SUFFIX@">0</token>
-  <token name="@PROFILE@">22.01</token>
+  <token name="@PROFILE@">21.05</token>
   <xml name="version_command">
      <version_command><![CDATA[rcf -V]]></version_command>
   </xml>
diff -r 856d50c93de9 -r b135c5908e8c recentrifuge.xml
--- a/recentrifuge.xml	Wed Apr 06 10:34:16 2022 +0000
+++ b/recentrifuge.xml	Wed Apr 06 13:52:48 2022 +0000
@@ -365,25 +365,21 @@
       <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="20"/>
     </test>
   </tests>
-  <help><![CDATA[
+  <help>
+    <![CDATA[
     =-= /home/pierre/anaconda3/envs/rcf/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-=
-
   usage: rcf [-h] [-V] [-n PATH] [--format GENERIC_FORMAT]
              (-f FILE | -g FILE | -l FILE | -r FILE | -k FILE) [-o FILE]
              [-e OUTPUT_TYPE] [-p] [--nohtml] [-a | -c CONTROLS_NUMBER]
              [-s SCORING] [-y NUMBER] [-m INT] [-x TAXID] [-i TAXID] [-z NUMBER]
              [-w INT] [-u SUMMARY_BEHAVIOR] [-t] [--nokollapse] [-d] [--strain]
              [--sequential]
-
   Robust comparative analysis and contamination removal for metagenomics
-
   options:
     -h, --help            show this help message and exit
     -V, --version         show program's version number and exit
-
   input:
     Define Recentrifuge input files and formats
-
     -n PATH, --nodespath PATH
                           path for the nodes information files (nodes.dmp and
                           names.dmp from NCBI)
@@ -419,10 +415,8 @@
                           every .krk file inside will be taken as a different
                           sample; multiple -k is available to include several
                           Kraken (version 1 or 2) samples
-
   output:
     Related to the Recentrifuge output files
-
     -o FILE, --outprefix FILE
                           output prefix; if not given, it will be inferred from
                           input files; an HTML filename is still accepted for
@@ -434,10 +428,8 @@
                           pandas DataFrames (format affected by selection of
                           --extra)
     --nohtml              suppress saving the HTML output file
-
   tuning:
     Coarse tuning of algorithm parameters
-
     -a, --avoidcross      avoid cross analysis
     -c CONTROLS_NUMBER, --controls CONTROLS_NUMBER
                           this number of first samples will be treated as
@@ -460,10 +452,8 @@
                           NCBI taxid code to include a taxon and all underneath
                           (multiple -i is available to include several taxid);
                           by default, all the taxa are considered for inclusion
-
   fine tuning:
     Fine tuning of algorithm parameters
-
     -z NUMBER, --ctrlminscore NUMBER
                           minimum score/confidence of the classification of a
                           read in control samples to pass the quality filter; it
@@ -477,33 +467,28 @@
                           ['ADD', 'ONLY', 'AVOID']
     -t, --takeoutroot     remove counts directly assigned to the "root" level
     --nokollapse          show the "cellular organisms" taxon
-
   advanced:
     Advanced modes of running
-
     -d, --debug           increase output verbosity and perform additional
                           checks
     --strain              set strain level instead of species as the resolution
                           limit for the robust contamination removal algorithm;
                           use with caution, this is an experimental feature
     --sequential          deactivate parallel processing
-
   rcf - Release 1.8.1 - Mar 2022
-
       Copyright (C) 2017–2022, Jose Manuel Martí Martínez
-
       This program is free software: you can redistribute it and/or modify
       it under the terms of the GNU Affero General Public License as
       published by the Free Software Foundation, either version 3 of the
       License, or (at your option) any later version.
-
       This program is distributed in the hope that it will be useful,
       but WITHOUT ANY WARRANTY; without even the implied warranty of
       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
       GNU Affero General Public License for more details.
-
       You should have received a copy of the GNU Affero General Public License
       along with this program.  If not, see <https://www.gnu.org/licenses/>.
-    ]]></help>
-    <expand macro="citations"/>
-    </tool>
+      
+    ]]>
+  </help>
+  <expand macro="citations"/>
+</tool>