add: gotree reformat #7052
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| --- | ||
| description: gotree toolkit | ||
| categories: | ||
| - Phylogenetics | ||
| owner: iuc | ||
| homepage_url: https://github.com/evolbioinfo/gotree | ||
| long_description: | | ||
| Gotree is a set of command line tools to manipulate phylogenetic trees | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gotree | ||
| type: unrestricted | ||
| auto_tool_repositories: | ||
| name_template: "{{ tool_id }}" | ||
| description_template: "Wrapper for gotree {{ tool_name }}." | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| @@ -0,0 +1,95 @@ | ||||||||||||||||||
| <tool id="gotree_reformat" name="gotree reformat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> | ||||||||||||||||||
| <description>Convert phylogenetic trees between Nexus/NHX, Newick and phyloxml formats.</description> | ||||||||||||||||||
| <macros> | ||||||||||||||||||
| <import>macros.xml</import> | ||||||||||||||||||
| </macros> | ||||||||||||||||||
| <expand macro="xrefs"/> | ||||||||||||||||||
| <expand macro="requirements"/> | ||||||||||||||||||
| <expand macro="version_command"/> | ||||||||||||||||||
|
|
||||||||||||||||||
| <command detect_errors="exit_code"><![CDATA[ | ||||||||||||||||||
| #set format=$input_tree.file_ext | ||||||||||||||||||
| case "$format" in | ||||||||||||||||||
| newick) TREEFORMAT="newick" ;; | ||||||||||||||||||
| nex) TREEFORMAT="nexus" ;; | ||||||||||||||||||
| nexus) TREEFORMAT="nexus" ;; | ||||||||||||||||||
| phyloxml) TREEFORMAT="phyloxml" ;; | ||||||||||||||||||
| json) TREEFORMAT="nextstrain" ;; | ||||||||||||||||||
| *) echo "Unknown format: \$TREEFORMAT" && exit 1 ;; | ||||||||||||||||||
|
There was a problem hiding this comment. This should be |
||||||||||||||||||
| esac && | ||||||||||||||||||
|
|
||||||||||||||||||
| gotree reformat $output_format | ||||||||||||||||||
| --input $input_tree | ||||||||||||||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||||||||||||||
| --input-format \$TREEFORMAT | ||||||||||||||||||
| --output ./output.tree | ||||||||||||||||||
|
There was a problem hiding this comment. couldn't you write to There was a problem hiding this comment. or, more modern style: keep writing to There was a problem hiding this comment. see @bgruening 's original suggestion. |
||||||||||||||||||
| --threads \${GALAXY_SLOTS:-1} && | ||||||||||||||||||
|
|
||||||||||||||||||
| mv ./output.tree '$output_tree' | ||||||||||||||||||
|
|
||||||||||||||||||
| ]]></command> | ||||||||||||||||||
|
|
||||||||||||||||||
| <inputs> | ||||||||||||||||||
| <param name="input_tree" | ||||||||||||||||||
| type="data" | ||||||||||||||||||
| format="newick,nex,phyloxml,json" | ||||||||||||||||||
| label="Input tree" | ||||||||||||||||||
| help="Accepted formats: newick, nexus, phyloxml, nextstrain (json)" /> | ||||||||||||||||||
|
|
||||||||||||||||||
| <param name="output_format" | ||||||||||||||||||
| type="select" | ||||||||||||||||||
| label="Select output tree format"> | ||||||||||||||||||
| <option value="newick">Newick</option> | ||||||||||||||||||
| <option value="nexus">Nexus</option> | ||||||||||||||||||
| <option value="phyloxml">Phyloxml</option> | ||||||||||||||||||
| </param> | ||||||||||||||||||
| </inputs> | ||||||||||||||||||
|
|
||||||||||||||||||
| <outputs> | ||||||||||||||||||
| <data name="output_tree" format="txt" label="${tool.name} on ${on_string}"> | ||||||||||||||||||
| <change_format> | ||||||||||||||||||
| <when input="output_format" value="newick" format="newick" /> | ||||||||||||||||||
| <when input="output_format" value="nexus" format="nex" /> | ||||||||||||||||||
| <when input="output_format" value="phyloxml" format="phyloxml" /> | ||||||||||||||||||
| </change_format> | ||||||||||||||||||
| </data> | ||||||||||||||||||
| </outputs> | ||||||||||||||||||
|
|
||||||||||||||||||
| <tests> | ||||||||||||||||||
| <!-- Test 1: Convert from Newick to Nexus --> | ||||||||||||||||||
| <test expect_num_outputs="1"> | ||||||||||||||||||
| <param name="input_tree" value="test.newick" ftype="newick"/> | ||||||||||||||||||
ammaraziz marked this conversation as resolved.
Show resolved
Hide resolved
|
||||||||||||||||||
| <param name="output_format" value="nexus" /> | ||||||||||||||||||
| <output name="output_tree" file="newick-to.nex"> | ||||||||||||||||||
| <assert_contents> <has_text text="#NEXUS"/> </assert_contents> | ||||||||||||||||||
| </output> | ||||||||||||||||||
| </test> | ||||||||||||||||||
|
|
||||||||||||||||||
| <!-- Test 2: Convert from Nexus to PhyloXML --> | ||||||||||||||||||
| <test expect_num_outputs="1"> | ||||||||||||||||||
| <param name="input_tree" value="test.nex" ftype="nex"/> | ||||||||||||||||||
| <param name="output_format" value="phyloxml" /> | ||||||||||||||||||
| <output name="output_tree" file="newick-to.xml"> | ||||||||||||||||||
| <assert_contents> <has_text text="phylogeny rooted="/> </assert_contents> | ||||||||||||||||||
|
There was a problem hiding this comment.
Suggested change
There was a problem hiding this comment. Please check indentation here |
||||||||||||||||||
| </output> | ||||||||||||||||||
| </test> | ||||||||||||||||||
|
|
||||||||||||||||||
| <!-- Test 3: Convert from PhyloXML to Newick --> | ||||||||||||||||||
| <test expect_num_outputs="1"> | ||||||||||||||||||
| <param name="input_tree" value="test.xml" ftype="phyloxml"/> | ||||||||||||||||||
| <param name="output_format" value="newick" /> | ||||||||||||||||||
| <output name="output_tree" file="phylo-to.newick" > | ||||||||||||||||||
|
There was a problem hiding this comment. from https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests-test-output:
Since you're already doing a There was a problem hiding this comment. What you could add, however, to There was a problem hiding this comment.
Suggested change
There was a problem hiding this comment. Just saw that you've been using You should then also remove the test files from the PR altogether since they won't be used anyway. Depending on why exactly you needed |
||||||||||||||||||
| <assert_contents> <has_text text="(((hCoV-19"/> </assert_contents> | ||||||||||||||||||
| </output> | ||||||||||||||||||
|
Comment on lines
+80
to
+82
There was a problem hiding this comment.
Suggested change
|
||||||||||||||||||
| </test> | ||||||||||||||||||
| </tests> | ||||||||||||||||||
|
|
||||||||||||||||||
| <help><![CDATA[ | ||||||||||||||||||
| **GoTree Reformat** | ||||||||||||||||||
| Reformats an input tree file into different formats. | ||||||||||||||||||
|
|
||||||||||||||||||
| Input formats: Nexus, Newick, Phyloxml or Nextstrain | ||||||||||||||||||
| Output formats: Newick, Nexus or Phyloxml | ||||||||||||||||||
| ]]></help> | ||||||||||||||||||
|
|
||||||||||||||||||
| <expand macro="citations" /> | ||||||||||||||||||
| </tool> | ||||||||||||||||||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,25 @@ | ||||||
| <?xml version="1.0"?> | ||||||
| <macros> | ||||||
| <token name="@TOOL_VERSION@">0.4.5</token> | ||||||
| <token name="@VERSION_SUFFIX@">0</token> | ||||||
| <xml name="requirements"> | ||||||
| <requirements> | ||||||
| <requirement type="package" version="@TOOL_VERSION@">gotree</requirement> | ||||||
| </requirements> | ||||||
| </xml> | ||||||
| <xml name="version_command"> | ||||||
| <version_command>gotree version</version_command> | ||||||
| </xml> | ||||||
| <xml name="xrefs"> | ||||||
| <xrefs> | ||||||
| <xref type="bio.tools">Gotree</xref> | ||||||
|
There was a problem hiding this comment.
Suggested change
It's the unique bio.tools ID that you need to refer to, not the displayed name. No idea whether this is case-sensitive, but better play it safe. |
||||||
| </xrefs> | ||||||
| </xml> | ||||||
| <xml name="citations"> | ||||||
| <citations> | ||||||
| <citation type="doi">10.1093/nargab/lqab075</citation> | ||||||
| <yield /> | ||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||
| </citations> | ||||||
| </xml> | ||||||
| </macros> | ||||||
|
|
||||||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| #NEXUS | ||
| BEGIN TAXA; | ||
| DIMENSIONS NTAX=12; | ||
| TAXLABELS hCoV-19/Australia/QLD0x01518C/2025 hCoV-19/Denmark/DCGC-691554/2025 hCoV-19/Denmark/DCGC-691606/2025 hCoV-19/Finland/THL-02373/2025 hCoV-19/Germany/NW-RKI-I-1147997/2025 hCoV-19/Malaysia/MKAI-6710920/2025 hCoV-19/Netherlands/OV-RIVM-145269/2025 hCoV-19/Scotland/CLIMB-CM7YJPPK/2024 hCoV-19/Singapore/Y25R9MSC35/2025 hCoV-19/Sweden/T-60300744/2025 hCoV-19/Sweden/Y-22_SE100_25CS500200/2025 hCoV-19/Thailand/NIC_BKK_84/2025; | ||
| END; | ||
| BEGIN TREES; | ||
| TREE tree0 = (((hCoV-19/Australia/QLD0x01518C/2025:0.07699999999999818,(hCoV-19/Thailand/NIC_BKK_84/2025:0.04399999999986903,hCoV-19/Singapore/Y25R9MSC35/2025:0.021999999999934516):0.14500000000020918):0.06599999999980355,(hCoV-19/Malaysia/MKAI-6710920/2025:0.20199999999999818,(hCoV-19/Germany/NW-RKI-I-1147997/2025:0.24299999999993815,hCoV-19/Finland/THL-02373/2025:0.2899999999999636):0.02200000000016189):0.027999999999792635):0.026000000000067303,((hCoV-19/Netherlands/OV-RIVM-145269/2025:0.30599999999981264,(hCoV-19/Denmark/DCGC-691554/2025:0.038000000000010914,hCoV-19/Denmark/DCGC-691606/2025:0.038000000000010914):0.04899999999997817):0.018000000000029104,(hCoV-19/Scotland/CLIMB-CM7YJPPK/2024:0.04500000000007276,(hCoV-19/Sweden/T-60300744/2025:0.05499999999983629,hCoV-19/Sweden/Y-22_SE100_25CS500200/2025:0.3869999999999436):0.02500000000009095):0.021999999999934516):0.01700000000005275); | ||
| END; |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" | ||
| xmlns="http://www.phyloxml.org"> | ||
| <phylogeny rooted="true"> | ||
| <clade> | ||
| <clade> | ||
| <branch_length>0.000249121</branch_length> | ||
| <clade> | ||
| <branch_length>0.0000829749</branch_length> | ||
| <clade> | ||
| <branch_length>0.0000531102</branch_length> | ||
| <clade> | ||
| <branch_length>0.000152922</branch_length> | ||
| <clade> | ||
| <branch_length>0.0000107679</branch_length> | ||
| <clade> | ||
| <branch_length>0.0000700188</branch_length> | ||
| <clade> | ||
| <name>'MN346698.1|chimp|Cote_dIvoire||2017'</name> | ||
| <branch_length>0.0000540728</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <name>'KJ136820.1|chimp|Cote_dIvoire||2012'</name> | ||
| <branch_length>0.0000211467</branch_length> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <name>'DQ011156.1|monkey|Liberia||1970'</name> | ||
| <branch_length>0.0000105738</branch_length> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <name>'KP849470.1|human|Cote_dIvoire||1971'</name> | ||
| <branch_length>0.0000845594</branch_length> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <name>'AY741551.1|human|Sierra_Leone||'</name> | ||
| <branch_length>0.000183429</branch_length> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <name>'MT724769.1|swamp_rat|DRC||2012'</name> | ||
| <branch_length>0.000194718</branch_length> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <name>'MT903346.1|pouched_rat|USA||2003'</name> | ||
| <branch_length>0.000384278</branch_length> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.000414804</branch_length> | ||
| <clade> | ||
| <name>'KJ642615|human|Nigeria||1978'</name> | ||
| <branch_length>0.000271011</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.000690131</branch_length> | ||
| <clade> | ||
| <name>'KJ642617|human|Nigeria|Abia|1971-04-14'</name> | ||
| <branch_length>0.0000368402</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.000142185</branch_length> | ||
| <clade> | ||
| <name>'MK783027|human|Nigeria|Rivers|2017-11-09'</name> | ||
| <branch_length>0.0000211831</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.0000631634</branch_length> | ||
| <clade> | ||
| <name>'MK783033|human|Nigeria|Rivers|2017-10-09'</name> | ||
| <branch_length>0.000047712</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <name>'OP413718|human|United_Kingdom||2022-08'</name> | ||
| <branch_length>0.000189545</branch_length> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.0000684319</branch_length> | ||
| <clade> | ||
| <name>'MN648051|human|Israel|ex_Nigeria|2018-10-04'</name> | ||
| <branch_length>0.0000210763</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.000231667</branch_length> | ||
| <clade> | ||
| <name>'ON563414|human|USA||2022-05-19'</name> | ||
| <branch_length>0.0000000001</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <name>'OP415257|human|United_Kingdom|ex_Nigeria|2022-08'</name> | ||
| <branch_length>0.0000210588</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.000259498</branch_length> | ||
| <clade> | ||
| <name>'B1.fastq.gz'</name> | ||
| <branch_length>0.0000377656</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <name>'B2.fastq.gz'</name> | ||
| <branch_length>0.0000466743</branch_length> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </phylogeny> | ||
| </phyloxml> |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| (((hCoV-19/Australia/QLD0x01518C/2025:0.07699999999999818,(hCoV-19/Thailand/NIC_BKK_84/2025:0.04399999999986903,hCoV-19/Singapore/Y25R9MSC35/2025:0.021999999999934516):0.14500000000020918):0.06599999999980355,(hCoV-19/Malaysia/MKAI-6710920/2025:0.20199999999999818,(hCoV-19/Germany/NW-RKI-I-1147997/2025:0.24299999999993815,hCoV-19/Finland/THL-02373/2025:0.2899999999999636):0.02200000000016189):0.027999999999792635):0.026000000000067303,((hCoV-19/Netherlands/OV-RIVM-145269/2025:0.30599999999981264,(hCoV-19/Denmark/DCGC-691554/2025:0.038000000000010914,hCoV-19/Denmark/DCGC-691606/2025:0.038000000000010914):0.04899999999997817):0.018000000000029104,(hCoV-19/Scotland/CLIMB-CM7YJPPK/2024:0.04500000000007276,(hCoV-19/Sweden/T-60300744/2025:0.05499999999983629,hCoV-19/Sweden/Y-22_SE100_25CS500200/2025:0.3869999999999436):0.02500000000009095):0.021999999999934516):0.01700000000005275); |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| (((hCoV-19/Australia/QLD0x01518C/2025:0.07699999999999818,(hCoV-19/Thailand/NIC_BKK_84/2025:0.04399999999986903,hCoV-19/Singapore/Y25R9MSC35/2025:0.021999999999934516):0.14500000000020918):0.06599999999980355,(hCoV-19/Malaysia/MKAI-6710920/2025:0.20199999999999818,(hCoV-19/Germany/NW-RKI-I-1147997/2025:0.24299999999993815,hCoV-19/Finland/THL-02373/2025:0.2899999999999636):0.02200000000016189):0.027999999999792635):0.026000000000067303,((hCoV-19/Netherlands/OV-RIVM-145269/2025:0.30599999999981264,(hCoV-19/Denmark/DCGC-691554/2025:0.038000000000010914,hCoV-19/Denmark/DCGC-691606/2025:0.038000000000010914):0.04899999999997817):0.018000000000029104,(hCoV-19/Scotland/CLIMB-CM7YJPPK/2024:0.04500000000007276,(hCoV-19/Sweden/T-60300744/2025:0.05499999999983629,hCoV-19/Sweden/Y-22_SE100_25CS500200/2025:0.3869999999999436):0.02500000000009095):0.021999999999934516):0.01700000000005275):0; |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| #NEXUS | ||
| begin trees; | ||
| tree tree_1 = [&R] ((((((('MN346698.1|chimp|Cote_dIvoire||2017':5.40728e-05,'KJ136820.1|chimp|Cote_dIvoire||2012':2.11467e-05)[&label="Node7"]:7.00188e-05,'DQ011156.1|monkey|Liberia||1970':1.05738e-05)[&label="Node6"]:1.07679e-05,'KP849470.1|human|Cote_dIvoire||1971':8.45594e-05)[&label="Node5"]:0.000152922,'AY741551.1|human|Sierra_Leone||':0.000183429)[&label="Node4"]:5.31102e-05,'MT724769.1|swamp_rat|DRC||2012':0.000194718)[&label="Node3"]:8.29749e-05,'MT903346.1|pouched_rat|USA||2003':0.000384278)[&label="Node2"]:0.000249121,('KJ642615|human|Nigeria||1978':0.000271011,('KJ642617|human|Nigeria|Abia|1971-04-14':3.68402e-05,('MK783027|human|Nigeria|Rivers|2017-11-09':2.11831e-05,('MK783033|human|Nigeria|Rivers|2017-10-09':4.77120e-05,'OP413718|human|United_Kingdom||2022-08':0.000189545)[&label="Node12"]:6.31634e-05,('MN648051|human|Israel|ex_Nigeria|2018-10-04':2.10763e-05,('ON563414|human|USA||2022-05-19':1.00000e-10,'OP415257|human|United_Kingdom|ex_Nigeria|2022-08':2.10588e-05,('B1.fastq.gz':3.77656e-05,'B2.fastq.gz':4.66743e-05)[&label="Node16"]:0.000259498)[&label="Node14"]:0.000231667)[&label="Node13"]:6.84319e-05)[&label="Node10"]:0.000142185)[&label="Node9"]:0.000690131)[&label="Node8"]:0.000414804)[&label="Node1"]; | ||
| end; |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" | ||
| xmlns="http://www.phyloxml.org"> | ||
| <phylogeny rooted="true"> | ||
| <clade> | ||
| <clade> | ||
| <branch_length>0.026000000000067303</branch_length> | ||
| <clade> | ||
| <branch_length>0.06599999999980355</branch_length> | ||
| <clade> | ||
| <name>hCoV-19/Australia/QLD0x01518C/2025</name> | ||
| <branch_length>0.07699999999999818</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.14500000000020918</branch_length> | ||
| <clade> | ||
| <name>hCoV-19/Thailand/NIC_BKK_84/2025</name> | ||
| <branch_length>0.04399999999986903</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <name>hCoV-19/Singapore/Y25R9MSC35/2025</name> | ||
| <branch_length>0.021999999999934516</branch_length> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.027999999999792635</branch_length> | ||
| <clade> | ||
| <name>hCoV-19/Malaysia/MKAI-6710920/2025</name> | ||
| <branch_length>0.20199999999999818</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.02200000000016189</branch_length> | ||
| <clade> | ||
| <name>hCoV-19/Germany/NW-RKI-I-1147997/2025</name> | ||
| <branch_length>0.24299999999993815</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <name>hCoV-19/Finland/THL-02373/2025</name> | ||
| <branch_length>0.2899999999999636</branch_length> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.01700000000005275</branch_length> | ||
| <clade> | ||
| <branch_length>0.018000000000029104</branch_length> | ||
| <clade> | ||
| <name>hCoV-19/Netherlands/OV-RIVM-145269/2025</name> | ||
| <branch_length>0.30599999999981264</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.04899999999997817</branch_length> | ||
| <clade> | ||
| <name>hCoV-19/Denmark/DCGC-691554/2025</name> | ||
| <branch_length>0.038000000000010914</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <name>hCoV-19/Denmark/DCGC-691606/2025</name> | ||
| <branch_length>0.038000000000010914</branch_length> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.021999999999934516</branch_length> | ||
| <clade> | ||
| <name>hCoV-19/Scotland/CLIMB-CM7YJPPK/2024</name> | ||
| <branch_length>0.04500000000007276</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <branch_length>0.02500000000009095</branch_length> | ||
| <clade> | ||
| <name>hCoV-19/Sweden/T-60300744/2025</name> | ||
| <branch_length>0.05499999999983629</branch_length> | ||
| </clade> | ||
| <clade> | ||
| <name>hCoV-19/Sweden/Y-22_SE100_25CS500200/2025</name> | ||
| <branch_length>0.3869999999999436</branch_length> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </clade> | ||
| </phylogeny> | ||
| </phyloxml> |
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.