comparison test-data/test2_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

0:3a24265075bd

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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


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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/>.

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command used: integron_finder /tmp/tmpz_euzvww/files/e/9/9/dataset_e996a731-6537-452b-87d7-09654e6d628a.dat --cpu 1 --keep-tmp --local-max -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40

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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     : - 1 complete integron(s) found with a total 3 attC site(s)
INFO     : - 0 CALIN element(s) found with a total of 0 attC site(s)
INFO     : - 0 In0 element(s) found with a total of 0 attC site
INFO     : Starting search with local_max...:
INFO     : Search with local_max done... :
INFO     : In replicon ACBA.007.P01_13, there are:
INFO     : - 1 complete integron(s) found with a total 4 attC site(s)
INFO     : - 0 CALIN element(s) found with a total of 0 attC site(s)
INFO     : - 0 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.