| Previous changeset 3:b5407cc2bf51 (2023-08-31) Next changeset 5:76bf12b928f4 (2024-02-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge commit fbb5d7bb68cbb5f497cdda3c0697b21b046a8262 |
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modified:
macro.xml test-data/centrifuge_test/test2_csv.log test-data/centrifuge_test/test2_csv.rcf.data.csv test-data/centrifuge_test/test4_rcf.data.tsv test-data/centrifuge_test/test4_tsv.html test-data/kraken_test/test1_csv.log test-data/kraken_test/test1_csv.rcf.data.csv test-data/kraken_test/test1_csv.rcf.html test-data/kraken_test/test3_rcf.data.tsv test-data/kraken_test/test3_tsv.log |
| b |
| 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 |
| b |
| @@ -1,6 +1,6 @@ <?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"> |
| b |
| 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 =-= [90mCentrifuge .out files to analyze:[0m ['input_dir/centrifuge_out.out'] [90mLoading NCBI nodes...[0m[92m OK! [0m @@ -21,7 +21,7 @@ [0m[93m Warning![0m 210 orphan taxids[90m (rerun with --debug for details) [0minput_dir/centrifuge_out[94m sample [0m[92mOK! -[0m[90mLoad elapsed time: [0m0.0337[90m sec +[0m[90mLoad elapsed time: [0m0.0232[90m sec [0m [90m Building the taxonomy multiple tree... [0m[92mOK![0m |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| [ |
| b'@@ -74,7 +74,7 @@\n // \n //----------------------------------------------------------------------------\n //\n-// Copyright (C) 2017-2022 Jose Manuel Mart\xc3\xad Mart\xc3\xadnez, for the changes in\n+// Copyright (C) 2017-2024 Jose Manuel Mart\xc3\xad Mart\xc3\xadnez, for the changes in\n // this file from the Krona Javascript 2.0 release.\n //\n // Redistribution and use in source and binary forms, with or without\n@@ -4999,6 +4999,7 @@\n datasets = datasetNames.length;\n break;\n \n+ case \'n\':\n case \'node\':\n head = loadTreeDOM\n (\n@@ -5052,6 +5053,7 @@\n fontSize = Number(pair[1]);\n break;\n \n+ case \'n\':\n case \'node\':\n nodeDefault = Number(pair[1]);\n break;\n@@ -5108,6 +5110,9 @@\n if (domNode.getAttribute(\'href\')) {\n newNode.href = domNode.getAttribute(\'href\');\n }\n+ else {\n+ newNode.href = \'https://www.google.com/search?q=\' + newNode.name\n+ }\n \n if (hueName) {\n newNode.hues = new Array();\n@@ -5115,6 +5120,7 @@\n \n for (var i = getFirstChild(domNode); i; i = getNextSibling(i)) {\n switch (i.tagName.toLowerCase()) {\n+ case \'n\':\n case \'node\':\n var newChild = loadTreeDOM\n (\n@@ -6578,4 +6584,4 @@\n \t\tselectedNodeLast.getDepth() < selectedNode.getDepth());\n }\n */</script></head><body><img id="hiddenImage" src="data:image/png;base64,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" style="display:none"><img id="loadingImage" src="data:image/gif;base64,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" style="display:none"><img id="logo" src="data:image/png;base64,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'..b'><val href="1">1</val></tid><rnk><val>no_rank</val></rnk><sco><val>392.59</val><val>392.59</val><val>392.59</val><val>488.35</val><val>489.00</val><val>446.66</val><val>442.05</val><val>440.73</val><val>440.73</val><val>440.73</val></sco><n name="Bacteria"><cnt><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val>75</val><val>75</val></cnt><una><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val></una><tid><val href="2">2</val></tid><rnk><val>superkingdom</val></rnk><sco><val>392.59</val><val>392.59</val><val>392.59</val><val>488.35</val><val>489.00</val><val>446.66</val><val>442.05</val><val>440.73</val><val>440.73</val><val>440.73</val></sco><n name="Proteobacteria"><cnt><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val>75</val><val>75</val></cnt><una><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val>75</val><val></val></una><tid><val href="1224">1224</val></tid><rnk><val>phylum</val></rnk><sco><val>392.59</val><val>392.59</val><val>392.59</val><val>488.35</val><val>489.00</val><val>446.66</val><val>442.05</val><val>440.73</val><val>440.73</val><val>440.73</val></sco><n name="Gammaproteobacteria"><cnt><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val></val><val>75</val></cnt><una><val>2</val><val>2</val><val>2</val><val></val><val></val><val></val><val></val><val>75</val><val></val><val>2</val></una><tid><val href="1236">1236</val></tid><rnk><val>class</val></rnk><sco><val>392.59</val><val>392.59</val><val>392.59</val><val>488.35</val><val>489.00</val><val>446.66</val><val>442.05</val><val>440.73</val><val>0</val><val>440.73</val></sco><n name="Enterobacteriales"><cnt><val>73</val><val>73</val><val>73</val><val>31</val><val>35</val><val>67</val><val>73</val><val></val><val></val><val>73</val></cnt><una><val>6</val><val>6</val><val>6</val><val></val><val></val><val></val><val>73</val><val></val><val></val><val>6</val></una><tid><val href="91347">91347</val></tid><rnk><val>order</val></rnk><sco><val>390.56</val><val>390.56</val><val>390.56</val><val>488.35</val><val>489.00</val><val>446.66</val><val>442.05</val><val>0</val><val>0</val><val>442.05</val></sco><n name="Enterobacteriaceae"><cnt><val>67</val><val>67</val><val>67</val><val>31</val><val>35</val><val>67</val><val></val><val></val><val></val><val>67</val></cnt><una><val>32</val><val>32</val><val>32</val><val></val><val></val><val>67</val><val></val><val></val><val></val><val>32</val></una><tid><val href="543">543</val></tid><rnk><val>family</val></rnk><sco><val>400.34</val><val>400.34</val><val>400.34</val><val>488.35</val><val>489.00</val><val>446.66</val><val>0</val><val>0</val><val>0</val><val>446.66</val></sco><n name="Escherichia"><cnt><val>35</val><val>35</val><val>35</val><val>31</val><val>35</val><val></val><val></val><val></val><val></val><val>35</val></cnt><una><val>4</val><val>4</val><val>4</val><val></val><val>35</val><val></val><val></val><val></val><val></val><val>4</val></una><tid><val href="561">561</val></tid><rnk><val>genus</val></rnk><sco><val>494.03</val><val>494.03</val><val>494.03</val><val>488.35</val><val>489.00</val><val>0</val><val>0</val><val>0</val><val>0</val><val>489.00</val></sco><n name="Escherichia coli"><cnt><val>31</val><val>31</val><val>31</val><val>31</val><val></val><val></val><val></val><val></val><val></val><val>31</val></cnt><una><val>31</val><val>31</val><val>31</val><val>31</val><val></val><val></val><val></val><val></val><val></val><val>31</val></una><tid><val href="562">562</val></tid><rnk><val>species</val></rnk><sco><val>488.35</val><val>488.35</val><val>488.35</val><val>488.35</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>488.35</val></sco></n></n></n></n></n></n></n></n></krona></div></body></html>\n\\ No newline at end of file\n' |
| b |
| 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 =-= [90mKraken .krk files to analyze:[0m ['input_dir/kraken_out.krk'] [90mLoading NCBI nodes...[0m[92m OK! [0m @@ -22,7 +22,7 @@ [0m[93m Warning![0m 11 orphan taxids[90m (rerun with --debug for details) [0minput_dir/kraken_out[94m sample [0m[92mOK! -[0m[90mLoad elapsed time: [0m0.00392[90m sec +[0m[90mLoad elapsed time: [0m0.00283[90m sec [0m [90m Building the taxonomy multiple tree... [0m[92mOK![0m |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| [ |
| b'@@ -74,7 +74,7 @@\n // \n //----------------------------------------------------------------------------\n //\n-// Copyright (C) 2017-2022 Jose Manuel Mart\xc3\xad Mart\xc3\xadnez, for the changes in\n+// Copyright (C) 2017-2024 Jose Manuel Mart\xc3\xad Mart\xc3\xadnez, for the changes in\n // this file from the Krona Javascript 2.0 release.\n //\n // Redistribution and use in source and binary forms, with or without\n@@ -4999,6 +4999,7 @@\n datasets = datasetNames.length;\n break;\n \n+ case \'n\':\n case \'node\':\n head = loadTreeDOM\n (\n@@ -5052,6 +5053,7 @@\n fontSize = Number(pair[1]);\n break;\n \n+ case \'n\':\n case \'node\':\n nodeDefault = Number(pair[1]);\n break;\n@@ -5108,6 +5110,9 @@\n if (domNode.getAttribute(\'href\')) {\n newNode.href = domNode.getAttribute(\'href\');\n }\n+ else {\n+ newNode.href = \'https://www.google.com/search?q=\' + newNode.name\n+ }\n \n if (hueName) {\n newNode.hues = new Array();\n@@ -5115,6 +5120,7 @@\n \n for (var i = 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href="1">1</val></tid><rnk><val>no_rank</val></rnk><sco><val>13.61</val></sco><n name="Bacteria"><cnt><val>9</val></cnt><una><val></val></una><tid><val href="2">2</val></tid><rnk><val>superkingdom</val></rnk><sco><val>13.61</val></sco><n name="Proteobacteria"><cnt><val>9</val></cnt><una><val></val></una><tid><val href="1224">1224</val></tid><rnk><val>phylum</val></rnk><sco><val>13.61</val></sco><n name="Gammaproteobacteria"><cnt><val>9</val></cnt><una><val></val></una><tid><val href="1236">1236</val></tid><rnk><val>class</val></rnk><sco><val>13.61</val></sco><n name="Enterobacteriales"><cnt><val>9</val></cnt><una><val></val></una><tid><val href="91347">91347</val></tid><rnk><val>order</val></rnk><sco><val>13.61</val></sco><n name="Enterobacteriaceae"><cnt><val>9</val></cnt><una><val>9</val></una><tid><val href="543">543</val></tid><rnk><val>family</val></rnk><sco><val>13.61</val></sco></n></n></n></n></n></n></krona></div></body></html>\n\\ No newline at end of file\n' |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 =-= [93mCAUTION![0m --strain experimental mode activated! [90mKraken .krk files to analyze:[0m ['input_dir/kraken_out.krk'] @@ -23,7 +23,7 @@ [0m[93m Warning![0m 11 orphan taxids[90m (rerun with --debug for details) [0minput_dir/kraken_out[94m sample [0m[92mOK! -[0m[90mLoad elapsed time: [0m0.00395[90m sec +[0m[90mLoad elapsed time: [0m0.00424[90m sec [0m [90m Building the taxonomy multiple tree... [0m[92mOK![0m |