# HG changeset patch # User iuc # Date 1706202163 0 # Node ID 12f0968f171cd20f8444c3f735f48c2231683fd9 # Parent b5407cc2bf51809701aa475e9d5a23226d58c330 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge commit fbb5d7bb68cbb5f497cdda3c0697b21b046a8262 diff -r b5407cc2bf51 -r 12f0968f171c macro.xml --- a/macro.xml Thu Aug 31 04:46:52 2023 +0000 +++ b/macro.xml Thu Jan 25 17:02:43 2024 +0000 @@ -1,6 +1,6 @@ - 1.12.1 + 1.13.2 0 21.05 diff -r b5407cc2bf51 -r 12f0968f171c test-data/centrifuge_test/test2_csv.log --- a/test-data/centrifuge_test/test2_csv.log Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/centrifuge_test/test2_csv.log Thu Jan 25 17:02:43 2024 +0000 @@ -1,5 +1,5 @@ -=-= /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!  @@ -21,7 +21,7 @@  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! diff -r b5407cc2bf51 -r 12f0968f171c test-data/centrifuge_test/test2_csv.rcf.data.csv --- a/test-data/centrifuge_test/test2_csv.rcf.data.csv Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/centrifuge_test/test2_csv.rcf.data.csv Thu Jan 25 17:02:43 2024 +0000 @@ -1,5 +1,5 @@ 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 diff -r b5407cc2bf51 -r 12f0968f171c test-data/centrifuge_test/test4_rcf.data.tsv --- a/test-data/centrifuge_test/test4_rcf.data.tsv Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/centrifuge_test/test4_rcf.data.tsv Thu Jan 25 17:02:43 2024 +0000 @@ -1,5 +1,5 @@ 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 diff -r b5407cc2bf51 -r 12f0968f171c test-data/centrifuge_test/test4_tsv.html --- a/test-data/centrifuge_test/test4_tsv.html Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/centrifuge_test/test4_tsv.html Thu Jan 25 17:02:43 2024 +0000 @@ -74,7 +74,7 @@ // //---------------------------------------------------------------------------- // -// Copyright (C) 2017-2022 Jose Manuel Martí Martínez, for the changes in +// Copyright (C) 2017-2024 Jose Manuel Martí Martínez, for the changes in // this file from the Krona Javascript 2.0 release. // // Redistribution and use in source and binary forms, with or without @@ -4999,6 +4999,7 @@ datasets = datasetNames.length; break; + case 'n': case 'node': head = loadTreeDOM ( @@ -5052,6 +5053,7 @@ fontSize = Number(pair[1]); break; + case 'n': case 'node': nodeDefault = Number(pair[1]); break; @@ -5108,6 +5110,9 @@ if (domNode.getAttribute('href')) { newNode.href = domNode.getAttribute('href'); } + else { + newNode.href = 'https://www.google.com/search?q=' + newNode.name + } if (hueName) { newNode.hues = new Array(); @@ -5115,6 +5120,7 @@ for (var i = getFirstChild(domNode); i; i = getNextSibling(i)) { switch (i.tagName.toLowerCase()) { + case 'n': case 'node': var newChild = loadTreeDOM ( @@ -6578,4 +6584,4 @@ selectedNodeLast.getDepth() < selectedNode.getDepth()); } */
countunassignedtidrankscoreinput_dir/centrifuge_1_outinput_dir/centrifuge_2_outinput_dir/centrifuge_outSHARED_speciesSHARED_genusSHARED_familySHARED_orderSHARED_classSHARED_phylumSHARED_SUMMARY 757575313567737575751no_rank392.6392.6392.6488.4489.0446.7442.0440.7440.7440.7757575313567737575752superkingdom392.6392.6392.6488.4489.0446.7442.0440.7440.7440.775757531356773757575751224phylum392.6392.6392.6488.4489.0446.7442.0440.7440.7440.77575753135677375752227521236class392.6392.6392.6488.4489.0446.7442.0440.70440.7737373313567737366673691347order390.6390.6390.6488.4489.0446.7442.000442.0676767313567673232326732543family400.3400.3400.3488.4489.0446.7000446.7353535313535444354561genus494.0494.0494.0488.4489.00000489.031313131313131313131562species488.4488.4488.4488.400000488.4
\ No newline at end of file +" style="display:none">
cntunatidrnkscoinput_dir/centrifuge_1_outinput_dir/centrifuge_2_outinput_dir/centrifuge_outSHARED_speciesSHARED_genusSHARED_familySHARED_orderSHARED_classSHARED_phylumSHARED_SUMMARY 757575313567737575751no_rank392.59392.59392.59488.35489.00446.66442.05440.73440.73440.73757575313567737575752superkingdom392.59392.59392.59488.35489.00446.66442.05440.73440.73440.7375757531356773757575751224phylum392.59392.59392.59488.35489.00446.66442.05440.73440.73440.737575753135677375752227521236class392.59392.59392.59488.35489.00446.66442.05440.730440.73737373313567737366673691347order390.56390.56390.56488.35489.00446.66442.0500442.05676767313567673232326732543family400.34400.34400.34488.35489.00446.66000446.66353535313535444354561genus494.03494.03494.03488.35489.000000489.0031313131313131313131562species488.35488.35488.35488.3500000488.35
\ No newline at end of file diff -r b5407cc2bf51 -r 12f0968f171c test-data/kraken_test/test1_csv.log --- a/test-data/kraken_test/test1_csv.log Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/kraken_test/test1_csv.log Thu Jan 25 17:02:43 2024 +0000 @@ -1,5 +1,5 @@ -=-= /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!  @@ -22,7 +22,7 @@  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! diff -r b5407cc2bf51 -r 12f0968f171c test-data/kraken_test/test1_csv.rcf.data.csv --- a/test-data/kraken_test/test1_csv.rcf.data.csv Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/kraken_test/test1_csv.rcf.data.csv Thu Jan 25 17:02:43 2024 +0000 @@ -1,5 +1,5 @@ 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 diff -r b5407cc2bf51 -r 12f0968f171c test-data/kraken_test/test1_csv.rcf.html --- a/test-data/kraken_test/test1_csv.rcf.html Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/kraken_test/test1_csv.rcf.html Thu Jan 25 17:02:43 2024 +0000 @@ -74,7 +74,7 @@ // //---------------------------------------------------------------------------- // -// Copyright (C) 2017-2022 Jose Manuel Martí Martínez, for the changes in +// Copyright (C) 2017-2024 Jose Manuel Martí Martínez, for the changes in // this file from the Krona Javascript 2.0 release. // // Redistribution and use in source and binary forms, with or without @@ -4999,6 +4999,7 @@ datasets = datasetNames.length; break; + case 'n': case 'node': head = loadTreeDOM ( @@ -5052,6 +5053,7 @@ fontSize = Number(pair[1]); break; + case 'n': case 'node': nodeDefault = Number(pair[1]); break; @@ -5108,6 +5110,9 @@ if (domNode.getAttribute('href')) { newNode.href = domNode.getAttribute('href'); } + else { + newNode.href = 'https://www.google.com/search?q=' + newNode.name + } if (hueName) { newNode.hues = new Array(); @@ -5115,6 +5120,7 @@ for (var i = getFirstChild(domNode); i; i = getNextSibling(i)) { switch (i.tagName.toLowerCase()) { + case 'n': case 'node': var newChild = loadTreeDOM ( @@ -6578,4 +6584,4 @@ selectedNodeLast.getDepth() < selectedNode.getDepth()); } */
countunassignedtidrankscoreinput_dir/kraken_out 91no_rank13.692superkingdom13.691224phylum13.691236class13.6991347order13.699543family13.6
\ No newline at end of file +" style="display:none">
cntunatidrnkscoinput_dir/kraken_out 91no_rank13.6192superkingdom13.6191224phylum13.6191236class13.61991347order13.6199543family13.61
\ No newline at end of file diff -r b5407cc2bf51 -r 12f0968f171c test-data/kraken_test/test3_rcf.data.tsv --- a/test-data/kraken_test/test3_rcf.data.tsv Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/kraken_test/test3_rcf.data.tsv Thu Jan 25 17:02:43 2024 +0000 @@ -1,5 +1,5 @@ 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 diff -r b5407cc2bf51 -r 12f0968f171c test-data/kraken_test/test3_tsv.log --- a/test-data/kraken_test/test3_tsv.log Thu Aug 31 04:46:52 2023 +0000 +++ b/test-data/kraken_test/test3_tsv.log Thu Jan 25 17:02:43 2024 +0000 @@ -1,5 +1,5 @@ -=-= /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'] @@ -23,7 +23,7 @@  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!