add: gotree reformat #7052

ammaraziz · 2025-06-15T07:44:42Z

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
License permits unrestricted use (educational + commercial)
This PR adds a new tool or tool collection
This PR updates an existing tool or tool collection
This PR does something else (explain below)

bgruening

Thanks @ammaraziz

tools/gotree/gotree-reformat.xml

pvanheus

Thanks for the wrapper - I've noted some areas of suggested improvement (in addition to the .shed.yml that is missing)

tools/gotree/gotree-reformat.xml

pvanheus · 2025-06-15T08:44:58Z

On the question of "nextstrain format", it might be worth adding this to Galaxy. Here is a description of this format: https://docs.nextstrain.org/projects/auspice/en/stable/releases/v2.html and AuspiceJson would be a subclass of the Json datatype. On adding a datatype: https://docs.galaxyproject.org/en/master/dev/data_types.html

pvanheus · 2025-06-15T09:26:38Z

On the question of "nextstrain format", it might be worth adding this to Galaxy. Here is a description of this format: https://docs.nextstrain.org/projects/auspice/en/stable/releases/v2.html and AuspiceJson would be a subclass of the Json datatype. On adding a datatype: https://docs.galaxyproject.org/en/master/dev/data_types.html

Here's my PR for adding the "auspicejson" format: galaxyproject/galaxy#20466

tools/gotree/.shed.yml

tools/gotree/macros.xml

ammaraziz · 2025-06-19T03:58:12Z

Apologies, I forgot to switch branches when I committed the above fixes for another tool

bgruening · 2025-06-19T06:14:16Z

@ammaraziz do you see our comments above?

ammaraziz · 2025-06-19T23:37:35Z

@bgruening I do see them! and will work on them today. I made an error pushing code changes from another branch into this one causing issues I had to revert, thus the above comment (but it seems like my fixes remove the commit history, which is good).

Co-authored-by: Saim Momin <[email protected]>

Co-authored-by: Björn Grüning <[email protected]>

ammaraziz · 2025-06-20T00:50:30Z

On the question of "nextstrain format", it might be worth adding this to Galaxy. Here is a description of this format: https://docs.nextstrain.org/projects/auspice/en/stable/releases/v2.html and AuspiceJson would be a subclass of the Json datatype. On adding a datatype: https://docs.galaxyproject.org/en/master/dev/data_types.html

Here's my PR for adding the "auspicejson" format: galaxyproject/galaxy#20466

Amazing thanks Peter. I'll add nextstrain format as an output for now in anticipation of acceptance.

edit: scratch that, might be best to keep json format for now.

ammaraziz · 2025-06-23T05:17:57Z

@pvanheus @bgruening @SaimMomin12 All comments incorporated.

Ready for final review?

tools/gotree/gotree-reformat.xml

pvanheus

Just this one last change, and then I'm happy.

pvanheus · 2025-06-25T08:14:44Z

tools/gotree/gotree-reformat.xml

+          nexus) TREEFORMAT="nexus" ;;
+          phyloxml) TREEFORMAT="phyloxml" ;;
+          json) TREEFORMAT="nextstrain" ;;
+          *) echo "Unknown format: \$TREEFORMAT" && exit 1 ;;


This should be echo "Unknown format: $format" because at this point TREEFORMAT has not been set.

SaimMomin12

Thanks @ammaraziz for amending changes. Some minor changes inline and I think then we are ready for the merge.

SaimMomin12 · 2025-06-25T08:24:38Z

tools/gotree/.shed.yml

+---
+description: gotree toolkit
+categories:


Suggested change

---

description: gotree toolkit

categories:

description: gotree toolkit

categories:

SaimMomin12 · 2025-06-25T08:25:50Z

tools/gotree/gotree-reformat.xml

+        <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>


Suggested change

<assert_contents> <has_text text="phylogeny rooted="/> </assert_contents>

<assert_contents>

<has_text text="phylogeny rooted="/>

</assert_contents>

Please check indentation here

SaimMomin12 · 2025-06-25T08:26:05Z

tools/gotree/gotree-reformat.xml

+        <output name="output_tree" file="phylo-to.newick" >
+          <assert_contents> <has_text text="(((hCoV-19"/> </assert_contents>
+        </output>


Suggested change

<output name="output_tree" file="phylo-to.newick" >

<assert_contents> <has_text text="(((hCoV-19"/> </assert_contents>

</output>

<output name="output_tree" file="phylo-to.newick" >

<assert_contents>

<has_text text="(((hCoV-19"/>

</assert_contents>

</output>

SaimMomin12 · 2025-06-25T08:27:53Z

tools/gotree/macros.xml

+  <xml name="citations">
+      <citations>
+          <citation type="doi">10.1093/nargab/lqab075</citation>
+          <yield />


Suggested change

<yield />

wm75

Thanks a lot for contributing @ammaraziz 💛

wm75 · 2025-06-25T08:56:11Z

tools/gotree/gotree-reformat.xml

+      esac &&
+
+      gotree reformat $output_format
+      --input $input_tree


Suggested change

--input $input_tree

--input '$input_tree'

wm75 · 2025-06-25T08:59:03Z

tools/gotree/gotree-reformat.xml

+      gotree reformat $output_format
+      --input $input_tree
+      --input-format \$TREEFORMAT
+      --output ./output.tree


couldn't you write to '$output_tree' directly and save the mv?

or, more modern style: keep writing to ./output.tree, but let Galaxy handle the file transfer by using from_work_dir in <outputs><data>.

see @bgruening 's original suggestion.

wm75 · 2025-06-25T09:09:13Z

tools/gotree/macros.xml

+  </xml>
+  <xml name="xrefs">
+    <xrefs>
+      <xref type="bio.tools">Gotree</xref>


Suggested change

<xref type="bio.tools">Gotree</xref>

<xref type="bio.tools">gotree</xref>

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.

wm75 · 2025-06-25T09:13:15Z

tools/gotree/gotree-reformat.xml

+    <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" >


from https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests-test-output:

The functional test framework will execute the tool using the parameters defined in the tag sets and generate a temporary file, which will either be compared with the file named in the file attribute value or checked against assertions made by a child assert_contents tag

Since you're already doing a file-based exact comparison in this and all other tests, you shouldn't use any <assert_contents>.

What you could add, however, to <output> is the ftype attribute to check that not only the right content is produced but that the expected output format is set by Galaxy, too.

Suggested change

<output name="output_tree" file="phylo-to.newick" >

<output name="output_tree" file="phylo-to.newick" ftype="phyloxml" />

Just saw that you've been using sim_size before. So if an exact match is not what you want, you can remove the file check and keep only the <assert_contents> (just don't use both simultaneously).

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 sim_size a check with re_match_multiline as the comparison method may also be helpful.

ammaraziz added 4 commits June 15, 2025 17:42

gotree reformat v1

10032c1

added .shed.yml

5b2f23b

fixed shed file

51508e8

fixed shed

fa82c7c

bgruening reviewed Jun 15, 2025

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pvanheus reviewed Jun 15, 2025

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SaimMomin12 reviewed Jun 16, 2025

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ammaraziz force-pushed the main branch from 7f1b911 to fa82c7c Compare June 19, 2025 04:03

ammaraziz and others added 3 commits June 20, 2025 09:40

Update tools/gotree/.shed.yml

dc1b67b

Co-authored-by: Saim Momin <[email protected]>

Update tools/gotree/gotree-reformat.xml

8c18f1e

Co-authored-by: Björn Grüning <[email protected]>

Update tools/gotree/gotree-reformat.xml

91afeec

Co-authored-by: Björn Grüning <[email protected]>

v2; tests, code changes

aeda564

pvanheus reviewed Jun 23, 2025

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v3; code improvments

dfdfb1c

pvanheus approved these changes Jun 25, 2025

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pvanheus requested changes Jun 25, 2025

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SaimMomin12 reviewed Jun 25, 2025

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wm75 reviewed Jun 25, 2025

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	<xref type="bio.tools">Gotree</xref>
	<xref type="bio.tools">gotree</xref>

	<output name="output_tree" file="phylo-to.newick" >
	<output name="output_tree" file="phylo-to.newick" ftype="phyloxml" />

add: gotree reformat #7052

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add: gotree reformat #7052

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pvanheus commented Jun 15, 2025 •

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