wrappers for ppanggolin all and ppanggolin msa #6645

thomas-lacroix · 2024-12-18T13:06:47Z

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)

bernt-matthias

Wonderful. Added a few comments.

bernt-matthias · 2024-12-19T09:28:30Z

tools/ppanggolin/.shed.yml

+homepage_url: https://ppanggolin.readthedocs.io/en/latest/
+long_description: |
+  Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors.
+remote_repository_url: https://github.com/labgem/PPanGGOLiN


I think this should point to the IUC repo. Use this one for homepage_url. The readthedocs URL might be cool to mention in the tool's help section.

Suggested change

remote_repository_url: https://github.com/labgem/PPanGGOLiN

remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin

tools/ppanggolin/.shed.yml

tools/ppanggolin/ppanggolin_all.xml

tools/ppanggolin/ppanggolin_msa.xml

…o ppanggolin

thomas-lacroix · 2025-01-14T10:04:52Z

Thanks @bernt-matthias , I implemented your suggestions, does it look good to you ? I couldn't get the validator to work for checking the consistency of the input files format, I didn't find a way to loop through multiple datasets or dataset collection and didn't find an example of such a validator. I implemented this check in the section by raising an exception. Best, Thomas

bernt-matthias · 2025-01-14T12:00:08Z

tools/ppanggolin/ppanggolin_all.xml

+            	#set extension_input_files = $file.ext
+            #else:
+                #if $file.ext != $extension_input_files:
+                    #raise Exception("All the genome files must be of similar format, either all genbank files or all fasta files.")


Not sure if raising an exception is a good idea. Have you tried what happens in such a case?

The exception appears in the history for each output files that have failed, see screenshot enclosed.

bernt-matthias · 2025-01-14T12:01:40Z

tools/ppanggolin/ppanggolin_all.xml

+                    #raise Exception("All the genome files must be of similar format, either all genbank files or all fasta files.")
+            	#end if
+            #end if
+            #set base_name = str($file.element_identifier).split('.')[0]


What happens if users have . in the identifiers. Maybe ".".join(str($file.element_identifier).split('.')[:-1])

tools/ppanggolin/ppanggolin_all.xml

thomas-lacroix · 2025-01-21T09:28:12Z

Hi @bernt-matthias
I am wondering, is there any more changes to do so this PR can be merged ? My todo list for this PR is empty but I might have missed something.
Best,
Thomas

bernt-matthias

Sorry for the delay and thanks for the ping. I gave the tool a final look and have a few minor suggestions and requests.

bernt-matthias · 2025-01-21T09:34:42Z

tools/ppanggolin/ppanggolin_all.xml

+        #import os
+


Suggested change

#import os

bernt-matthias · 2025-01-21T09:35:21Z

tools/ppanggolin/ppanggolin_all.xml

+        mkdir -p "./tmp_ppanggolin/organism_list" &&
+        mkdir -p "./tmp_ppanggolin/ln_input_genomes" &&
+
+        echo -n > "./tmp_ppanggolin/organism_list/organism.list" &&


Suggested change

echo -n > "./tmp_ppanggolin/organism_list/organism.list" &&

touch "./tmp_ppanggolin/organism_list/organism.list" &&

bernt-matthias · 2025-01-21T09:36:26Z

tools/ppanggolin/ppanggolin_all.xml

+            	#set extension_input_files = $file.ext
+            #else:
+                #if $file.ext != $extension_input_files:
+                    #raise Exception("All the genome files must be of similar format, either all genbank files or all fasta files.")


Suggested change

#raise Exception("All the genome files must be of similar format, either all genbank files or all fasta files.")

#raise Exception("All the genome files must be of the same datatype, either all genbank files or all fasta files.")

bernt-matthias · 2025-01-21T09:40:49Z

tools/ppanggolin/ppanggolin_all.xml

+            #set base_name = ".".join(str($file.element_identifier).split('.')[:-1])
+            echo -e '${base_name}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&


I think we should just assume that the user prepared the collection such that the element_identifiers are the desired sample names and do not make any changes. On collection creation users can choose to remove extensions.

Suggested change

#set base_name = ".".join(str($file.element_identifier).split('.')[:-1])

echo -e '${base_name}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&

echo -e '${file.element_identifier}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&

Thanks @bernt-matthias , I implemented all your recommendations except this one. This change uncovered a problem with PPanGGOLiN that happens for files that have a space in their name or for compressed files using Galaxy as the suffix " uncompressed" (the first char is a space) is sometimes added when choosing gzip files as input. My solution was to use :

#set base_name = str($file.element_identifier).replace(" ", "_") echo -e '${base_name}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&

What do you think ?

Seems fine. Maybe document this in the parameter/tool help.

bernt-matthias · 2025-01-21T09:49:16Z

tools/ppanggolin/ppanggolin_all.xml

+        <section name="advanced_pangenome_output_files" title="Advanced pangenome output files" expanded="False">
+            <param name="advanced_pangenome_optional_files" type="select" label="Add the following pangenome output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
+            	<!-- Basic files -->
+                <option value="output_gene_presence_absence" selected="true">Gene presence absence</option>
+                <option value="output_gene_families" selected="true">Gene families</option>
+                <option value="output_mean_persistent_duplication" selected="true">Mean persistent duplication</option>
+                <option value="output_matrix" selected="true">Matrix</option>
+            	<!-- plot files -->
+                <option value="output_Ushaped_plot" selected="true">Ushaped plot</option>
+                <option value="output_tile_plot" selected="true">Tile plot</option>
+            	<!-- graph files -->
+                <option value="output_pangenomeGraph_light_gexf" selected="true">PanGenome Graph Light (Gexf)</option>
+                <option value="output_pangenomeGraph_gexf" selected="true">PanGenome Graph (Gexf)</option>
+                <option value="output_pangenomeGraph_json" selected="true">PanGenome Graph (Json)</option>
+            	<!-- advanced files -->
+                <option value="output_summarize_spots" selected="true">Summarize spots</option>
+                <option value="output_spots" selected="true">Spots</option>
+                <option value="output_spot_borders" selected="true">Spot borders</option>
+                <option value="output_border_protein_genes" selected="true">Border protein genes</option>
+                <option value="output_modules_summary" selected="true">Modules summary</option>
+                <option value="output_modules_in_genomes" selected="true">Modules in genomes</option>
+                <option value="output_modules_spots" selected="true">Modules spots</option>
+                <option value="output_modules_RGP_lists" selected="true">Modules RGP lists</option>
+                <option value="output_functional_modules" selected="true">Functional modules</option>
+            </param>
+        </section>    


Suggested change

<section name="advanced_pangenome_output_files" title="Advanced pangenome output files" expanded="False">

<param name="advanced_pangenome_optional_files" type="select" label="Add the following pangenome output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >



<option value="output_gene_presence_absence" selected="true">Gene presence absence</option>

<option value="output_gene_families" selected="true">Gene families</option>

<option value="output_mean_persistent_duplication" selected="true">Mean persistent duplication</option>

<option value="output_matrix" selected="true">Matrix</option>



<option value="output_Ushaped_plot" selected="true">Ushaped plot</option>

<option value="output_tile_plot" selected="true">Tile plot</option>



<option value="output_pangenomeGraph_light_gexf" selected="true">PanGenome Graph Light (Gexf)</option>

<option value="output_pangenomeGraph_gexf" selected="true">PanGenome Graph (Gexf)</option>

<option value="output_pangenomeGraph_json" selected="true">PanGenome Graph (Json)</option>



<option value="output_summarize_spots" selected="true">Summarize spots</option>

<option value="output_spots" selected="true">Spots</option>

<option value="output_spot_borders" selected="true">Spot borders</option>

<option value="output_border_protein_genes" selected="true">Border protein genes</option>

<option value="output_modules_summary" selected="true">Modules summary</option>

<option value="output_modules_in_genomes" selected="true">Modules in genomes</option>

<option value="output_modules_spots" selected="true">Modules spots</option>

<option value="output_modules_RGP_lists" selected="true">Modules RGP lists</option>

<option value="output_functional_modules" selected="true">Functional modules</option>

</param>

</section>

<param name="advanced_pangenome_optional_files" type="select" label="Add the following pangenome output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >



<option value="output_gene_presence_absence" selected="true">Gene presence absence</option>

<option value="output_gene_families" selected="true">Gene families</option>

<option value="output_mean_persistent_duplication" selected="true">Mean persistent duplication</option>

<option value="output_matrix" selected="true">Matrix</option>



<option value="output_Ushaped_plot" selected="true">Ushaped plot</option>

<option value="output_tile_plot" selected="true">Tile plot</option>



<option value="output_pangenomeGraph_light_gexf" selected="true">PanGenome Graph Light (Gexf)</option>

<option value="output_pangenomeGraph_gexf" selected="true">PanGenome Graph (Gexf)</option>

<option value="output_pangenomeGraph_json" selected="true">PanGenome Graph (Json)</option>



<option value="output_summarize_spots" selected="true">Summarize spots</option>

<option value="output_spots" selected="true">Spots</option>

<option value="output_spot_borders" selected="true">Spot borders</option>

<option value="output_border_protein_genes" selected="true">Border protein genes</option>

<option value="output_modules_summary" selected="true">Modules summary</option>

<option value="output_modules_in_genomes" selected="true">Modules in genomes</option>

<option value="output_modules_spots" selected="true">Modules spots</option>

<option value="output_modules_RGP_lists" selected="true">Modules RGP lists</option>

<option value="output_functional_modules" selected="true">Functional modules</option>

</param>

Du you think that the typical user really needs all outputs (all seem to be selected). If yes, fine for me.

I discussed the topic of the many output files with the creator of PPanGGOLiN and he thinks it is better to leave the default output files are they are now.

bernt-matthias · 2025-01-21T09:50:35Z

tools/ppanggolin/ppanggolin_msa.xml

+<tool id="ppanggolin_msa" name="PPanGGOLiN msa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
+    <description>computes msa of pangenome's gene families</description>


should we capitalize MSA in the name and description.

bernt-matthias · 2025-01-21T09:51:46Z

tools/ppanggolin/.shed.yml

@@ -0,0 +1,11 @@
+name: ppanggolin


Can you modify the shed.yml file to a suite? Like here: https://github.com/galaxyproject/tools-iuc/blob/main/tools/ampvis2/.shed.yml

thomas-lacroix · 2025-01-22T08:33:36Z

Hi @bernt-matthias ,
My todo list for this PR is now empty, let me know if you see other areas to improve.
Best,
Thomas

bernt-matthias

Good to go?

thomas-lacroix · 2025-01-22T08:54:44Z

yes, good to go :)

thomas-lacroix added 3 commits December 18, 2024 14:02

wrappers for ppanggolin all and ppanggolin msa

6234ac5

update ppanggolin

bf810be

fixed warning planemo lint

c328fe3

bernt-matthias reviewed Dec 19, 2024

View reviewed changes

thomas-lacroix added 4 commits January 14, 2025 09:40

Merge branch 'main' of https://github.com/galaxyproject/tools-iuc int…

96ac984

…o ppanggolin

implemented PR suggestions

a9756a1

remove obsolete param type in tests

a30be5e

test msa fails, trying to debug

d355710

bernt-matthias reviewed Jan 14, 2025

View reviewed changes

thomas-lacroix added 4 commits January 14, 2025 14:25

added unsatisfactory validator

a1d819e

added ppanggolin_all test expect_failure mixed fasta genbank

af72e2e

test expect_failure, ftype can not be a list

04a62a5

removed unsatisfactory validator

57121b2

bernt-matthias reviewed Jan 21, 2025

View reviewed changes

thomas-lacroix added 2 commits January 21, 2025 18:15

peer review improvments

a30649f

added help Space is not allowed in filename

e968c3c

bernt-matthias approved these changes Jan 22, 2025

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bernt-matthias merged commit f51871d into galaxyproject:main Jan 22, 2025
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thomas-lacroix deleted the ppanggolin branch January 22, 2025 10:34

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wrappers for ppanggolin all and ppanggolin msa #6645

wrappers for ppanggolin all and ppanggolin msa #6645

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	remote_repository_url: https://github.com/labgem/PPanGGOLiN
	remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin

	echo -n > "./tmp_ppanggolin/organism_list/organism.list" &&
	touch "./tmp_ppanggolin/organism_list/organism.list" &&

	#raise Exception("All the genome files must be of similar format, either all genbank files or all fasta files.")
	#raise Exception("All the genome files must be of the same datatype, either all genbank files or all fasta files.")

		#set base_name = ".".join(str($file.element_identifier).split('.')[:-1])
		echo -e '${base_name}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&

	#set base_name = ".".join(str($file.element_identifier).split('.')[:-1])
	echo -e '${base_name}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&
	echo -e '${file.element_identifier}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&

		<tool id="ppanggolin_msa" name="PPanGGOLiN msa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
		<description>computes msa of pangenome's gene families</description>

wrappers for ppanggolin all and ppanggolin msa #6645

wrappers for ppanggolin all and ppanggolin msa #6645

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