New tool addition: amas tool #7443
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See updated changes from George at jchchiu#1 |
tools/amas/amas.xml
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| <param name="in_format" type="select" label="Format of the input file"> | ||
| <option value="fasta">fasta</option> | ||
| <option value="phylip">phylip</option> | ||
| <option value="phylip-int">phylip-int</option> | ||
| <option value="nexus">nexus(sequential)</option> | ||
| <option value="nexus-int">nexus(interleaved)</option> | ||
| </param> |
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fasta phylip and nexus can be distinguishe automatically, e.g. $input_file.ext gives the Galaxy datatype. Is the info on interleaved/not needed? Can it be determined automatically?
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It doesn't seem like they have a function that detects the format for interleaved automatically; instead it depends on the input you give it. Can galaxy automatically distinguish interleaved?
tools/amas/amas.xml
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| </collection> | ||
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| <collection name="converted_alignments" type="list" label="Converted alignments"> | ||
| <discover_datasets directory="run_dir/convert" pattern="(?P<name>.+)-out\..+" format="data" /> |
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We should set the format instead if format="data"
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Could you have a look at the amas_split.xml at L55; is this what you were thinking?
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Hey @bernt-matthias, could you have a look at amas_concat.xml and see if this is on the right track? If so, I'll update the rest of the subcommands with your suggestions. |
This reverts commit 6fc566f.
| concat | ||
| --concat-part partitions.txt | ||
| --concat-out concatenated.out | ||
| --part-format $part_format |
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You can determine the input format from $input_files.ext.
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Comment also relevant to #7443 (comment)
The problem I have with this is that if it is a nexus or phylip file, their extension doesn't always tell whether it is an interleaved or sequential format. Even if you sniff it as an interleaved does $input_files.ext return phlyip-int or something like that which differentiates it from normal phylip? Otherwise I'm pretty sure amas needs the user to explicitly set the file format as an input.
What are you thoughts on only taking non-interleaved formats, and give a warning to the user that it will not accept interleaved in the help or something? Following this also removing the option to output it as an interleaved file? Problem I see with this is that they can still upload an interleaved file since they have the same extension.
| help="A file defining how the concatenated alignment is split into separate gene/locus regions. Each line specifies a partition name and its position range (e.g., 'gene1 = 1-500' or 'DNA, gene1 = 1-500' for RAxML format)."> | ||
| <option value="nexus">nexus</option> | ||
| <option value="raxml">raxml</option> | ||
| <option value="unspecified" selected="true">unspecified</option> |
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What happens in the unspecified case?
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It just has the genes and their start and end; should I add more context or just direct them to the help section?
- Unspecified:
gene1 = 1-500 - RAxML:
DNA, gene1 = 1-500 - NEXUS:
#NEXUS
Begin sets;
charset gene1 = 1-500;
End;
| </xml> | ||
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| <xml name="version_command"> | ||
| <version_command>python -m amas.AMAS -h</version_command> |
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-h gives the version?
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Actually, I don't think there is any command in amas that gives the version. What do you suggest as the recommended procedure if there is no such version command? Tried a bit of searching but couldn't find anything.
Could try to open a PR on the tool to add a simple command but the repo doesn't seem active.
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You could just echo @TOOL_VERSION@
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Or even better python -c "import amas; print(amas.__version__)"
…d some formatting
tools/amas/amas_concat.xml
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| <when input="out_format" value="nexus-int" format="nex" /> | ||
| </change_format> | ||
| </data> | ||
| <data name="partitions_out" from_work_dir="run_dir/action/partitions.txt" format="txt" label="Partition file" /> |
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File extension is irrelevant. part_format determines the format, isn't it. You can then:
https://docs.galaxyproject.org/en/master/dev/schema.html#tool-outputs-data-change-format-when
| <param name="in_format" value="fasta" /> | ||
| <param name="data_type" value="dna" /> | ||
| <param name="check_align" value="false" /> | ||
| <output name="output" file="outputs/expected_concat.phylip" ftype="phylip" compare="sim_size" /> |
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Can we comp[are the content instead of "just" compare="sim_size"
| </xml> | ||
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| <xml name="version_command"> | ||
| <version_command>python -m amas.AMAS -h</version_command> |
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You could just echo @TOOL_VERSION@
| </inputs> | ||
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| <outputs> | ||
| <data name="summary_out" from_work_dir="summary.txt" format="txt" label="${tool.name} on ${on_string} (Alignment summary)" /> |
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Can you use a format like the following for all labels
<data name="summary_out" from_work_dir="summary.txt" format="txt" label="${tool.name} on ${on_string}: Alignment summary" />
| </xml> | ||
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| <xml name="version_command"> | ||
| <version_command>python -m amas.AMAS -h</version_command> |
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Or even better python -c "import amas; print(amas.__version__)"
3 participants
FOR CONTRIBUTOR:
Regarding issue #7442
To do:
For now, is it possible to review the code to see if it's on the right track, and if there are any better ways to structure it?