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Merge pull request galaxyproject#5731 from pimarin/recentrifuge
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update recentrifuge version to v1.13.2
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@bgruening
bgruening authored Jan 25, 2024
2 parents 7cbd5cb + 8fa1230 commit fbb5d7b
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Showing 10 changed files with 27 additions and 15 deletions.
2 changes: 1 addition & 1 deletion tools/recentrifuge/macro.xml
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<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">1.12.1</token>
<token name="@TOOL_VERSION@">1.13.2</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">21.05</token>
<xml name="version_command">
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4 changes: 2 additions & 2 deletions tools/recentrifuge/test-data/centrifuge_test/test2_csv.log
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=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-=
=-= /home/pierre/miniconda3/envs/__recentrifuge@1.13.2/bin/rcf =-= v1.13.2 - Jan 2024 =-= by Jose Manuel Martí =-=

Centrifuge .out files to analyze: ['input_dir/centrifuge_out.out']
Loading NCBI nodes... OK! 
Expand All @@ -21,7 +21,7 @@ Please, wait, processing files in parallel...

Warning! 210 orphan taxids (rerun with --debug for details)
input_dir/centrifuge_out sample OK!
Load elapsed time: 0.0337 sec
Load elapsed time: 0.0232 sec


Building the taxonomy multiple tree... OK!
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2 changes: 1 addition & 1 deletion tools/recentrifuge/test-data/centrifuge_test/test2_csv.rcf.data.csv
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Samples,input_dir/centrifuge_out,input_dir/centrifuge_out,input_dir/centrifuge_out,Details,Details
Stats,count,unassigned,score,Rank,Name
Stats,cnt,una,sco,Rank,Name
Id,,,,,
1,75,0,51.07625068955332,no_rank,root
2,75,0,51.07625068955332,superkingdom,Bacteria
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2 changes: 1 addition & 1 deletion tools/recentrifuge/test-data/centrifuge_test/test4_rcf.data.tsv
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Samples input_dir/centrifuge_1_out input_dir/centrifuge_1_out input_dir/centrifuge_1_out input_dir/centrifuge_2_out input_dir/centrifuge_2_out input_dir/centrifuge_2_out input_dir/centrifuge_out input_dir/centrifuge_out input_dir/centrifuge_out SHARED_species SHARED_species SHARED_species SHARED_genus SHARED_genus SHARED_genus SHARED_family SHARED_family SHARED_family SHARED_order SHARED_order SHARED_order SHARED_class SHARED_class SHARED_class SHARED_phylum SHARED_phylum SHARED_phylum SHARED_SUMMARY SHARED_SUMMARY SHARED_SUMMARY Details Details
Stats count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score Rank Name
Stats cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco Rank Name
Id
1 75 0 392.58666666666664 75 0 392.58666666666664 75 0 392.58666666666664 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 0 442.0475236076006 75 0 440.72856742250906 75 0 440.72856742250906 75 0 440.72856742250906 no_rank root
2 75 0 392.58666666666664 75 0 392.58666666666664 75 0 392.58666666666664 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 0 442.0475236076006 75 0 440.72856742250906 75 0 440.72856742250906 75 0 440.72856742250906 superkingdom Bacteria
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10 changes: 8 additions & 2 deletions tools/recentrifuge/test-data/centrifuge_test/test4_tsv.html
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4 changes: 2 additions & 2 deletions tools/recentrifuge/test-data/kraken_test/test1_csv.log
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=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-=
=-= /home/pierre/miniconda3/envs/__recentrifuge@1.13.2/bin/rcf =-= v1.13.2 - Jan 2024 =-= by Jose Manuel Martí =-=

Kraken .krk files to analyze: ['input_dir/kraken_out.krk']
Loading NCBI nodes... OK! 
Expand All @@ -22,7 +22,7 @@ Please, wait, processing files in parallel...

Warning! 11 orphan taxids (rerun with --debug for details)
input_dir/kraken_out sample OK!
Load elapsed time: 0.00392 sec
Load elapsed time: 0.00283 sec


Building the taxonomy multiple tree... OK!
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2 changes: 1 addition & 1 deletion tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.data.csv
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Samples,input_dir/kraken_out,input_dir/kraken_out,input_dir/kraken_out,Details,Details
Stats,count,unassigned,score,Rank,Name
Stats,cnt,una,sco,Rank,Name
Id,,,,,
1,9,0,13.614815253856928,no_rank,root
2,9,0,13.614815253856928,superkingdom,Bacteria
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10 changes: 8 additions & 2 deletions tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.html
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2 changes: 1 addition & 1 deletion tools/recentrifuge/test-data/kraken_test/test3_rcf.data.tsv
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Samples input_dir/kraken_out input_dir/kraken_out input_dir/kraken_out Details Details
Stats count unassigned score Rank Name
Stats cnt una sco Rank Name
Id
1 9 0 2.7230463906265316 no_rank root
2 9 0 2.7230463906265316 superkingdom Bacteria
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4 changes: 2 additions & 2 deletions tools/recentrifuge/test-data/kraken_test/test3_tsv.log
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=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-=
=-= /home/pierre/miniconda3/envs/__recentrifuge@1.13.2/bin/rcf =-= v1.13.2 - Jan 2024 =-= by Jose Manuel Martí =-=

CAUTION! --strain experimental mode activated!
Kraken .krk files to analyze: ['input_dir/kraken_out.krk']
Expand All @@ -23,7 +23,7 @@ Please, wait, processing files in parallel...

Warning! 11 orphan taxids (rerun with --debug for details)
input_dir/kraken_out sample OK!
Load elapsed time: 0.00395 sec
Load elapsed time: 0.00424 sec


Building the taxonomy multiple tree... OK!
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