New Addition: ripples and general update to latest version of usher #7306

lsterck · 2025-09-25T18:34:34Z

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)

This pull request adds the RIPPLES tool to the usher suit.
Since usher version was a 0.2.1 and RIPPLES only added in v 0.4.0, the whole package was updated to the latest version (0.6.6)
Extra options were added that were released in the past 4-5y , but perhaps not all of them

linked to issue #7242

bgruening

Cool, a few comments inline.

bgruening · 2025-09-29T19:46:45Z

tools/usher/matutils.xml

        matUtils
        $matutils_mode.options_mode
-        --input-mat $mutation_annotation_file
+        --input-mat '$mutation_annotation_file.name'


Suggested change

--input-mat '$mutation_annotation_file.name'

--input-mat '$mutation_annotation_file.element_identifier'

bgruening · 2025-09-29T19:47:16Z

tools/usher/matutils.xml

@@ -7,9 +7,12 @@
    <expand macro='requirements' />
    <version_command>usher --version</version_command>
    <command detect_errors='exit_code'><![CDATA[
+    ## get correct extension filenames
+     ln -sf '$mutation_annotation_file' '$mutation_annotation_file.name' &&


Suggested change

ln -sf '$mutation_annotation_file' '$mutation_annotation_file.name' &&

ln -sf '$mutation_annotation_file' '$mutation_annotation_file.element_identifier' &&

I'll look into it.
I think it specifically needs the correct extension ...

bgruening · 2025-09-29T19:48:19Z

tools/usher/matutils.xml

@@ -195,7 +216,7 @@
                    <option value="write-mat">Write the selected subtree as a mutation annotated tree (--write-math)</option>  
                    <option value="write-mat-collapsed">Write the selected subtree as a collapsed mutation annotated tree (--write-mat --collapsed)</option>  
                    <option value="write-json">Write an Auspice-compatbile json representing the selected subtree (--write-json)</option>  
-                    <option value="write-tree"> Write a newick string representing the selected subtree (--write-tree)</option>
+                    <option value="write-tree"> Write a newick strineg representing the selected subtree (--write-tree)</option>


that looks wrong now

🤦‍♂️ it sure does 🙂

bgruening

Upps forget to submit my review. Thanks @lsterck

bgruening · 2025-10-04T17:53:04Z

tools/usher/matutils.xml

@@ -1,4 +1,4 @@
-<tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='23.2'>
+<tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.02'>


Why such an old profile?

dunno
that was what was there before.
I thought this indicate the min version that was needed to run the software?

bgruening · 2025-10-04T17:53:58Z

tools/usher/matutils.xml

-            <output name="parent_placements" file="test_22_parent_placements.tabular" ftype="tabular"/>
+            <output name="parent_placements" ftype="tabular">
+                <assert_contents>
+                    <has_size value="199899" delta="300"/>


size comparisons are not good tests. They are not very stingent, can you assert some content? Or assert the line count, or column count?

Good thing you pointed me to change the test checks (though those tests were already there)
In the process of changing it to file checks it turned out there was a nasty bug hidden in one of the parameter processing causing that specific test to always fail (could technical not even be run) but since check on output size it passed the wrapper test.

bgruening · 2025-10-04T17:54:23Z

tools/usher/ripples.xml

+
+ ]]>    </command>
+    <inputs>
+        <param argument="--input-mat" type="data" format="protobuf3" label="Mutation-annotated tree object" help="Load a mutation annotated tree file, in protocol-buffers format (protobuf3)."/>


please consider adding min/max to all integers/float params

Would like to, but have no idea what sensible ranges would be ...
As I understand it is very dependent from the input/output trees used and as such it does not really make sense to "fix" ranges

bgruening · 2025-10-04T17:54:44Z

tools/usher/ripples.xml

+        <param argument="--num-descendants" type="integer" value="10" label="Number of descendants" help="Minimum number of leaves that node should have to be considered for recombinatino. Default = 10." />
    </inputs>
+    <outputs>
+        <data name="recombination" format="tabular" from_work_dir='recombination.tsv' label="${tool.name} on ${on_string}: recombinations" />


do you want to add metadata for the column names here?

lsterck · 2025-10-10T15:14:02Z

one test failed with :

History not found

what does that mean actually? @bgruening

anyway, maybe I should remove even more of those file_size checks

SaimMomin12 · 2025-10-13T14:02:22Z

one test failed with :

History not found

what does that mean actually? @bgruening

anyway, maybe I should remove even more of those file_size checks

Let me restart the CI

lsterck added 14 commits August 1, 2025 17:51

version update and initial addition ripples

de920ae

start of ripples addition

be50626

aded extra test output files

392ac5b

updated tools files to v 6.6

1927643

updated test data files

d26d227

update of test data files

805426c

added test files for ripples

d2e7faf

test non deterministic, updated for assert content

06836fe

test file renamed

7070fa7

addition of ripples tool file

d43bfb6

missing test file for ripples test

0d49338

typo fix

5292ac7

typo fix and update test file, matutils

19d6d7e

fake edit to invoke test again

d25847c

lsterck marked this pull request as ready for review September 28, 2025 20:20

bgruening reviewed Sep 29, 2025

View reviewed changes

review amending and some layout fixing

e09a68c

lsterck requested a review from bgruening October 1, 2025 07:08

bgruening reviewed Oct 4, 2025

View reviewed changes

lsterck added 5 commits October 10, 2025 11:44

improved test, now filechecks

a68cadb

bug fix in sanitizing input

09a175a

review fixing and other improvements

d80054c

deleted too big test files

ff0c24e

changed test to avoid to big files

5825dbf

lsterck requested a review from bgruening October 13, 2025 14:13

	--input-mat '$mutation_annotation_file.name'
	--input-mat '$mutation_annotation_file.element_identifier'

	ln -sf '$mutation_annotation_file' '$mutation_annotation_file.name' &&
	ln -sf '$mutation_annotation_file' '$mutation_annotation_file.element_identifier' &&

		@@ -1,4 +1,4 @@
		<tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='23.2'>
		<tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.02'>

New Addition: ripples and general update to latest version of usher #7306

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New Addition: ripples and general update to latest version of usher #7306

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lsterck commented Sep 25, 2025

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lsterck commented Oct 10, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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SaimMomin12 commented Oct 13, 2025

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