ampir Panaroo and Yara ToolFactory generated tools. #1326

fubar2 · 2023-09-01T11:47:20Z

adding first tested and working generated tool from the nf-core module to galaxy tool converter at https://github.com/fubar2/nftoolmaker

It passes planemo tests and lint. Generated by parsing the nf-core module yaml and using the ToolFactory to generate the XML.
Will need cleaning up - specific suggestions welcomed - changes will affect all future generated tools as I'd like to make them as consistent as possible with IUC guidelines that make sense for autogenerated tools.

The test data is a real challenge because it has to be extracted from special test descriptions written in their nextflow DDL.
Fortunately, most nf-core developers have line oriented habits making it possible to decompose these without needing a proper parser. Mind you, I did try - pyparsing is great but my skills were weak.
Where DSL trickery is used, the automation fails and the nextflow source can be fixed if needed so the tool will work.
However, in this trivial test case, it works completely automagically.
Hope this is useful to someone.

…m/fubar2/nftoolmaker It actually does work. Sort of. Hope this is useful to someone.

bgruening

Thanks Ross. Lets try to figure this out.

tools/ampir/.shed.yml

tools/ampir/ampir.xml

bgruening · 2023-09-01T12:46:45Z

tools/ampir/ampir.xml

+  <requirements>
+    <requirement version="1.1.0" type="package">r-ampir</requirement>
+  </requirements>
+  <stdio>


This very simple stdio is deprecated and should be replaced with <command detect_errors="aggressive">

That's the galaxyxml supplied default. Not trivial to fix but needs a galaxyxml PR to replace the default stdio addition and to add keywords to the <command> tag. More work than I need right now - can we live with it until galaxyxml is fixed?
Easy to replace the actual contents of the tag - for example, would this from one of bgruening's tools be better for an automated boilerplate stdio?

<stdio> <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> <exit_code range="137" level="fatal_oom" description="Out of Memory" /> <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> </stdio> </xml>

Just don't use it, put in a profile version for reasonable defaults.

bgruening · 2023-09-01T12:47:18Z

tools/ampir/ampir.xml

+  <stdio>
+    <exit_code range="1:" level="fatal"/>
+  </stdio>
+  <version_command><![CDATA[echo "0.01"]]></version_command>


mh, that should be ampir --version or something similar

Or in this case something like:

<version_command><![CDATA[Rscript -e 'library(vegan)' 2>&1 > /dev/null | grep 'This is vegan']]></version_command>

I have always wondered about this. The ToolFactory form allows one to be specified for manual building. However for automation, it's a little tricky....it will now echo the first Conda dependency version if given, or the supplied ToolFactory form version string for manual builds.

What should that "version" command report?

Should it report the tool XML/wrapper version? (makes most sense to me, giving all the other metadata)

If there are >1 conda package(s), is the first one the version?

What about a container?

For the record, every module script includes code to generate a fresh version.txt when run. It seems to be in every nf-core module. Unfortunately, sometimes it is buried inside an Rscript and sometimes it is part of the bash script. Either way, it's too complex to automate reliably. I could echo the conda version but that won't work for a container.
Suggestions or PR welcomed if anyone thinks it's a show-stopper.

This is not going to be simple or reliable to automate as your suggestion shows so some imperfect but good enough for nf-core (TM) fudging is called for.

Now uses the first conda dependency version if there is one, or else the tool version as the version string.
Does that work?

bgruening · 2023-09-01T12:49:27Z

tools/ampir/ampir_Rscript

@@ -0,0 +1,15 @@
+#!/usr/bin/env Rscript


that script is part of the configfile isn't it? Why is this included in the PR?

The user wanting to fix a converted module will need to get the script working first so it is supplied as a convenience - no need to copypasta - just setup a conda env and get it working on the command line - then it can be fixed in my nf-core module fork permanently so the next build run will work correctly.

Will permanently remove it if you think that's better - please let me know?

Tool generation produces a yaml file containing the generated command line.
Any ToolFactory instance can regenerate the tool because the TF will (soon) have a ToolFactory that accepts a yaml file as input instead of requiring a form to be filled in - but then the history job can be rerun and the form easily modifed so changes are easier. Will make those available on the github repository for ToolFactory users.

bgruening · 2023-09-01T12:52:09Z

tools/ampir/ampir.xml

+  <inputs>
+    <param name="faa" type="data" optional="false" label="FASTA file containing amino acid sequences" help="" format="fasta" multiple="false"/>
+    <param name="min_length" type="integer" value="10" label="Minimum protein length for which predictions will be generated" help=""/>
+    <param name="min_probability" type="float" value="0.7" label="Cut-off for AMP prediction" help=""/>


Can we add somehow min/max?

Possible only if there is a machine readable source of truth.
That is never specified for any parameter in any of the nf-core module stuff I have found. If you can suggest an automatable way, let me know. It's not part of the TF either and would make the form even more horribly complex so probably won't fix that.

bgruening · 2023-09-01T12:52:30Z

tools/ampir/ampir.xml

+  </inputs>
+  <outputs>
+    <data name="amps_faa" format="fasta" label="File containing AMP predictions in amino acid FASTA format" hidden="false"/>
+    <data name="amps_tsv" format="tsv" label="File containing AMP predictions in TSV format" hidden="false"/>


tsv should be tabular I think

tsv is indeed in datatypes_config

<datatype extension="tsv" type="galaxy.datatypes.tabular:TSV" display_in_upload="true"> <converter file="tabular_to_csv.xml" target_datatype="csv"/> </datatype>

nf-core to Galaxy formats is challenging. Needs a translate table so it is easy enough to convert tsv (they always use that) to tabular if you prefer ..... will do since it's easy.

bgruening · 2023-09-01T12:53:49Z

tools/ampir/ampir.xml

+    </test>
+  </tests>
+  <help><![CDATA[description: A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale.
+


what are we doing with the help? Fix manually and later keep it during merge?

Currently, it is grabbed from the yaml - can't really see any other useful sources but happy to use anything that you'd like to see.
This should all be automated. Manual fixes are not going to be part of these tools since the whole point is that they can be re-autogenerated whenever the underlying nf-core repository is updated in CI?

bgruening · 2023-09-01T12:54:38Z

tools/ampir/ampir.xml

+
+
+
+doi: 10.1093/bioinformatics/btaa653


this DOI is different from the one below

Yes.
It comes from the nf-core module yaml and correctly leads to https://pubmed.ncbi.nlm.nih.gov/32683445/
The other is the ToolFactory paper DOI.
Automating the nf-core doi is possible but it is not mandatory so messy - could be done if you want?

…ply to all future generated tools :)

fubar2 · 2023-09-02T01:05:14Z

Thanks @bgruening!
Changed the owner to me for these generated tools in .shed.yml and made all the suggested changes that are easy to automate.
Generating tools from nf-core spawn is very different from manually writing tools or manually filling in a ToolFactory form, so some small deficiencies are almost inevitable from the highly variable but generally not great quality of the inputs.

Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq

fubar2 · 2023-09-04T00:50:10Z

@bgruening
Yara was relatively easy to generate with the ToolFactory so is now added to this same PR.
It is a bugger of an executable because it insists on specific file extensions for information about what's incoming. Painful but I have worked around it and the ToolFactory coped well...
Let me know what you want to do so mthang can try Yara out please?
It maps :

single fasta
single fastq
paired fastq.

Anyone know why $foo.ext will return fastqsanger instead of fastq for a fastq in my history? It caused me hours of wasted time even though the data was definitely showing fastq not fastqsanger.. I noticed others have used startswith('fastq') so I used that....but it's a horrible hack for an odd wart.

fubar2 · 2023-09-04T01:15:26Z

grrrr - vanishing single quotes added back to give bash '$runme'

mvdbeek · 2023-09-04T07:46:37Z

tools/ampir/ampir.xml

@@ -0,0 +1,87 @@
+<tool name="ampir" id="ampir" version="1.1.0">


You definitely want a profile version here

I fixed it when @bgruening mentioned it but now I see it was in the wrong place :( Currently rebuilding everything.

<tool profile="22.05" name="yara_mapper" id="yara_mapper" version="1.17">  

now and for any future generated tool. Thanks @mvdbeek! Will upload in the morning. Been a long day.

@mvdbeek @bgruening - are these ok now?
Thanks for reviewing!

I only commented on the obvious stuff. You want to drop the stdio section too, drop the unused script, write a help section and address @bgruening's comments. I don't think the auto-generation should lower the usual threshold we have for IUC tools.

all these too @mvdbeek ?
Looks like most of them use stdio here, so am not sure how to understand your request, or which of @bgruening's comments remain unresolved. Help appreciated.

tools/openms/FidoAdapter.xml:11: <expand macro="stdio"/> tools/openms/RTEvaluation.xml:11: <expand macro="stdio"/> tools/openms/FeatureFinderMetabo.xml:11: <expand macro="stdio"/> tools/openms/OpenSwathDecoyGenerator.xml:11: <expand macro="stdio"/> tools/openms/FFEval.xml:11: <expand macro="stdio"/> tools/openms/OpenSwathWorkflow.xml:11: <expand macro="stdio"/> tools/openms/PTPredict.xml:11: <expand macro="stdio"/> tools/openms/ExternalCalibration.xml:11: <expand macro="stdio"/> tools/openms/CVInspector.xml:11: <expand macro="stdio"/> tools/openms/XTandemAdapter.xml:11: <expand macro="stdio"/> tools/openms/PhosphoScoring.xml:11: <expand macro="stdio"/> tools/openms/HighResPrecursorMassCorrector.xml:11: <expand macro="stdio"/> tools/openms/PeptideIndexer.xml:11: <expand macro="stdio"/> tools/openms/OpenSwathFileSplitter.xml:11: <expand macro="stdio"/> tools/openms/PeakPickerWavelet.xml:11: <expand macro="stdio"/> tools/openms/MapRTTransformer.xml:11: <expand macro="stdio"/> tools/openms/QCMerger.xml:11: <expand macro="stdio"/> tools/openms/MRMMapper.xml:11: <expand macro="stdio"/> tools/openms/SpectraMerger.xml:11: <expand macro="stdio"/> tools/openms/XMLValidator.xml:11: <expand macro="stdio"/> tools/openms/FeatureLinkerLabeled.xml:11: <expand macro="stdio"/> tools/openms/TransformationEvaluation.xml:11: <expand macro="stdio"/> tools/numeric_clustering/numeric_clustering.xml:6: <stdio> tools/augustus/augustus.xml:12: </stdio> tools/crt/crt.xml:8: <stdio> tools/quast/quast.xml:28: </stdio> tools/metilene/metilene.xml:12: <stdio> tools/metilene/metilene.xml:15: </stdio> tools/text_processing/text_processing/macros.xml:9: <xml name="stdio"> tools/minced/minced.xml:7: <stdio> tools/minced/minced.xml:10: </stdio> tools/format_cd_hit_output/format_cd_hit_output.xml:7: <stdio> tools/format_cd_hit_output/format_cd_hit_output.xml:9: </stdio> tools/rna_tools/miRDeep2/miRDeep2_quantifier/quantifier.xml:6: <stdio> tools/rna_tools/miRDeep2/miRDeep2_quantifier/quantifier.xml:13: </stdio> tools/rna_tools/cmv/cmcv.xml:7: <expand macro="stdio" /> tools/rna_tools/dotknot/dotknot.xml:12: </stdio> tools/rna_tools/infernal/cmstat.xml:7: <expand macro="stdio" /> tools/rna_tools/locarna/locarna_exparnap.xml:12: <expand macro="stdio" /> tools/rna_tools/vienna_rna/rnaplex.xml:9: <expand macro="stdio" /> tools/rna_tools/vienna_rna/rnaplot.xml:8: <expand macro="stdio" /> tools/rna_tools/ribotaper/ribotaper_part2_create_metaplots.xml:7: <stdio> tools/instagraal/instagraal.xml:22: </stdio> tools/GraphClust/Plotting/MotifFinderPlot.xml:7: <stdio> tools/GraphClust/Plotting/MotifFinderPlot.xml:9: </stdio> tools/GraphClust/PrepareForMlocarna/preMlocarna.xml:6: <stdio> tools/GraphClust/PrepareForMlocarna/preMlocarna.xml:8: </stdio> tools/GraphClust/NSPDK/NSPDK_sparseVect.xml:6: <stdio> tools/GraphClust/NSPDK/NSPDK_candidateClusters.xml:8: </stdio> tools/GraphClust/GSPAN/fasta2shrep_gspan.xml:6: <stdio> tools/GraphClust/GSPAN/fasta2shrep_gspan.xml:8: </stdio> tools/GraphClust/LocARNAGraphClust/locarna_best_subtree.xml:8: <stdio> tools/GraphClust/LocARNAGraphClust/locarna_best_subtree.xml:10: </stdio> tools/GraphClust/Preprocessing/preprocessing.xml:8: <stdio> tools/GraphClust/Preprocessing/preprocessing.xml:10: </stdio> tools/jamm/jamm.xml:28:<stdio> tools/jamm/jamm.xml:32:</stdio> tools/platypus/platypus.xml:6: <stdio> tools/image_processing/imagej2/imagej2_macros.xml:10: <stdio> tools/image_processing/imagej2/imagej2_macros.xml:15: </stdio> tools/EDeN/EDeN/EDeN_feature.xml:36: <stdio> tools/EDeN/EDeN/EDeN_feature.xml:41: </stdio> tools/twistdna/twistdna.xml:6: <stdio> tools/twistdna/twistdna.xml:9: </stdio> tools/protease_prediction/protease.xml:7: <expand macro="stdio"/> tools/protease_prediction/macros.xml:8: <xml name="stdio"> tools/protease_prediction/macros.xml:9: <stdio> tools/protease_prediction/macros.xml:11: </stdio> tools/labels/labels.xml:8: <stdio> tools/labels/labels.xml:13: </stdio> tools/ampir/ampir.xml:8: <stdio> tools/ampir/ampir.xml:12: </stdio> tools/sqlite_merger/sqlite_merger.xml:19: <stdio> tools/sqlite_merger/sqlite_merger.xml:24: </stdio> tools/mafft/mafft-add.xml:8: <stdio> tools/vt/vt_macros.xml:16: <xml name="stdio"> tools/vt/vt_macros.xml:17: <stdio> tools/vt/vt_macros.xml:22: </stdio> tools/vt/vt_macros.xml:22: </stdio> tools/vt/vt_macros.xml:22: </stdio> tools/vt/vt_normalize.xml:8: <expand macro="stdio" /> tools/vt/vt_decompose.xml:8: <expand macro="stdio" /> tools/bigwig_to_bedgraph/bigwig_to_bedgraph.xml:8: <stdio> tools/bigwig_to_bedgraph/bigwig_to_bedgraph.xml:10: </stdio> tools/sklearn/pre_process.xml:7: <expand macro="macro_stdio" /> tools/sklearn/feature_selection.xml:8: <expand macro="macro_stdio" /> tools/sklearn/to_categorical.xml:7: <expand macro="macro_stdio" /> tools/sklearn/model_prediction.xml:8: <expand macro="macro_stdio" /> tools/sklearn/discriminant.xml:8: <expand macro="macro_stdio" /> tools/sklearn/keras_macros.xml:4: <xml name="macro_stdio"> tools/sklearn/keras_macros.xml:5: <stdio> tools/sklearn/keras_macros.xml:7: </stdio> tools/sklearn/model_validation.xml:7: <expand macro="macro_stdio" /> tools/sklearn/regression_metrics.xml:7: <expand macro="macro_stdio" /> tools/sklearn/pca.xml:7: <expand macro="macro_stdio" /> tools/sklearn/label_encoder.xml:7: <expand macro="macro_stdio"/> tools/sklearn/nn_classifier.xml:7: <expand macro="macro_stdio" /> tools/sklearn/stacking_ensembles.xml:41: <expand macro="macro_stdio" /> tools/sklearn/fitted_model_eval.xml:8: <expand macro="macro_stdio" /> tools/sklearn/main_macros.xml:13: <xml name="macro_stdio"> tools/sklearn/main_macros.xml:14: <stdio> tools/sklearn/main_macros.xml:18: </stdio> tools/sklearn/numeric_clustering.xml:7: <expand macro="macro_stdio" /> tools/sklearn/lightgbm.xml:9: <expand macro="macro_stdio" /> tools/sklearn/simple_model_fit.xml:8: <expand macro="macro_stdio" /> tools/sklearn/association_rules.xml:7: <expand macro="macro_stdio"/> tools/sklearn/train_test_eval.xml:8: <expand macro="macro_stdio" /> tools/sklearn/svm.xml:8: <expand macro="macro_stdio" /> tools/sklearn/estimator_attributes.xml:7: <expand macro="macro_stdio" /> tools/sklearn/pairwise_metrics.xml:7: <expand macro="macro_stdio" /> tools/sklearn/train_test_split.xml:12: <expand macro="macro_stdio" /> tools/sklearn/pipeline.xml:7: <expand macro="macro_stdio" /> tools/sklearn/keras_train_and_eval.xml:8: <expand macro="macro_stdio" /> tools/sklearn/search_model_validation.xml:32: <expand macro="macro_stdio" /> tools/sklearn/generalized_linear.xml:7: <expand macro="macro_stdio" /> tools/sklearn/clf_metrics.xml:7: <expand macro="macro_stdio" /> tools/sklearn/keras_model_builder.xml:8: <expand macro="macro_stdio" /> tools/sklearn/sparse.xml:7: <expand macro="macro_stdio" /> tools/sklearn/ml_visualization_ex.xml:8: <expand macro="macro_stdio" /> tools/sklearn/keras_model_config.xml:8: <expand macro="macro_stdio" /> tools/sklearn/sample_generator.xml:7: <expand macro="macro_stdio" /> tools/sklearn/keras_batch_models.xml:8: <expand macro="macro_stdio" /> tools/sklearn/ensemble.xml:7: <expand macro="macro_stdio" /> tools/diff/diff.xml:11: <stdio> tools/diff/diff.xml:14: </stdio> tools/format_metaphlan2_output/format_metaphlan2_output.xml:7: <stdio> tools/format_metaphlan2_output/format_metaphlan2_output.xml:8: </stdio> data_managers/data_manager_sortmerna_database_downloader/data_manager/data_manager_sortmerna_download.xml:10: <stdio> data_managers/data_manager_sortmerna_database_downloader/data_manager/data_manager_sortmerna_download.xml:13: </stdio> chemicaltoolbox/openbabel/macros.xml:33: <xml name="stdio"> chemicaltoolbox/openbabel/macros.xml:34: <stdio> chemicaltoolbox/openbabel/macros.xml:36: </stdio> chemicaltoolbox/opsin/opsin.xml:7: <stdio> chemicaltoolbox/opsin/opsin.xml:12: </stdio> chemicaltoolbox/data_source/get_pubchem/get_pubchem_as_smiles.xml:7: <stdio> chemicaltoolbox/data_source/get_pubchem/get_pubchem_as_smiles.xml:20: </stdio> chemicaltoolbox/autodock_vina/prepare_ligand/prepare_ligand.xml:10: <stdio> chemicaltoolbox/autodock_vina/prepare_ligand/prepare_ligand.xml:12: </stdio> chemicaltoolbox/autodock_vina/prepare_receptor/prepare_receptor.xml:10: <stdio> chemicaltoolbox/autodock_vina/prepare_receptor/prepare_receptor.xml:12: </stdio>

No, just your new tool please. I can't review everything, and if you do need something special not covered by the defaults you will indeed need a stdio tag set.

@mvdbeek hexylena/galaxyxml#38 fixes it I think as far as is feasible adding detect_errors="aggressive" to the command tag. I copied that stdio from one of Bjoern's recent tools and see that most stull use it but am happy to lead the charge once the PR is in. Automated help is a stretch since the nf-core stuff has none to speak of, but the hand-crafted ones, panaroo and yara have handcrafted and I hope quite reasonable help from their documentation. Ampir is completely automated from the nf-core module and test. A different order of not IUC.

…dio replacement...

adding first tested and working generated tool from https://github.co…

6453a58

…m/fubar2/nftoolmaker It actually does work. Sort of. Hope this is useful to someone.

bgruening reviewed Sep 1, 2023

View reviewed changes

fixes suggested by bgruening for the PR - all adjustments will now ap…

fbcd261

…ply to all future generated tools :)

fubar2 added 2 commits September 4, 2023 10:29

add yara mapper ToolFactory - NOT from nf-core.

a5724a8

Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq

small test files still work :)

1566f5b

fubar2 changed the title ~~ampir: auto-generated tool from the nf-core module using a new ToolFactory based tool.~~ ampir: auto-generated tool from the nf-core module using a new ToolFactory based tool, and Yara: indexer/mapper from the ToolFactory. Sep 4, 2023

single quotes for $runme - disappeared mysteriously :(

9bce04a

fubar2 added 2 commits September 4, 2023 16:40

adding panaroo

4f2eccb

Finally fixed the '$runme' suggestion and got the sanitisers not to.

6734d07

fubar2 changed the title ~~ampir: auto-generated tool from the nf-core module using a new ToolFactory based tool, and Yara: indexer/mapper from the ToolFactory.~~ ampir Panaroo and Yara ToolFactory generated tools. Sep 4, 2023

mvdbeek reviewed Sep 4, 2023

View reviewed changes

fix profile="22.05" - need to update galaxyxml to fix this and the st…

4309858

…dio replacement...

fubar2 mentioned this pull request Sep 6, 2023

IUC want profile in the <tool> and detect_errors in the <command> hexylena/galaxyxml#38

Merged

Merge branch 'bgruening:master' into master

49dcace

fubar2 closed this Dec 14, 2023

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ampir Panaroo and Yara ToolFactory generated tools. #1326

ampir Panaroo and Yara ToolFactory generated tools. #1326

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		@@ -0,0 +1,87 @@
		<tool name="ampir" id="ampir" version="1.1.0">




		doi: 10.1093/bioinformatics/btaa653

ampir Panaroo and Yara ToolFactory generated tools. #1326

ampir Panaroo and Yara ToolFactory generated tools. #1326

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