diff test-data/test3_integron_log @ 0:3a24265075bd draft default tip

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/blob/master/tools/integron_finder commit 6b06711cfba45855d5a992ed1c73c472eaef644f

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+++ b/test-data/test3_integron_log	Mon Feb 13 13:53:43 2023 +0000
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+
+**************************************************************************
+ ___       _                               _____ _           _
+|_ _|_ __ | |_ ___  __ _ _ __ ___  _ __   |  ___(_)_ __   __| | ___ _ __
+ | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \  | |_  | | '_ \ / _` |/ _ \ '__|
+ | || | | | ||  __/ (_| | | | (_) | | | | |  _| | | | | | (_| |  __/ |
+|___|_| |_|\__\___|\__, |_|  \___/|_| |_| |_|   |_|_| |_|\__,_|\___|_|
+                   |___/
+
+**************************************************************************
+
+integron_finder version 2.0.2
+Using:
+ - Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50)  [GCC 10.3.0]
+ - numpy 1.19.4
+ - pandas 1.1.5
+ - matplolib 3.3.3
+ - biopython 1.78
+
+ - Prodigal V2.6.3: February, 2016
+ - INFERNAL 1.1.4 (Dec 2020)
+ - HMMER 3.3.2 (Nov 2020); http://hmmer.org/
+
+Authors:
+ - Jean Cury, Bertrand Neron, Eduardo Rocha,
+
+Citation:
+
+ Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C. 
+ IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. 
+ Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
+
+ If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
+
+ Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
+ PMID: 29112715
+
+
+                     =======================
+
+integron_finder is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+integron_finder 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 General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program (COPYING file).
+If not, see <http://www.gnu.org/licenses/>.
+
+                     =======================
+
+command used: integron_finder /tmp/tmpz_euzvww/files/4/3/f/dataset_43f32a10-119c-4fb5-bdaf-498b2d3b61b3.dat --cpu 1 --keep-tmp --linear -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+
+                     =======================
+
+
+INFO     : ############ Processing replicon ACBA.007.P01_13 (1/1) ############
+
+INFO     : Starting Default search ... :
+INFO     : Default search done... : 
+INFO     : In replicon ACBA.007.P01_13, there are:
+INFO     : - 0 complete integron(s) found with a total 0 attC site(s)
+INFO     : - 1 CALIN element(s) found with a total of 3 attC site(s)
+INFO     : - 1 In0 element(s) found with a total of 0 attC site
+INFO     : Adding proteins ... :
+INFO     : Writing out results for replicon ACBA.007.P01_13
+INFO     : Merging integrons results.
+