| Previous changeset 18:e4a053d67e24 (2023-09-01) Next changeset 20:6ab1a261520a (2024-07-28) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 |
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modified:
alphafold.xml scripts/validate_fasta.py |
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| diff -r e4a053d67e24 -r 2f7702fd0a4c alphafold.xml --- a/alphafold.xml Fri Sep 01 00:09:46 2023 +0000 +++ b/alphafold.xml Wed May 08 06:26:55 2024 +0000 |
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| @@ -3,7 +3,7 @@ <macros> <token name="@TOOL_VERSION@">2.3.1</token> <token name="@TOOL_MINOR_VERSION@">2.3</token> - <token name="@VERSION_SUFFIX@">4</token> + <token name="@VERSION_SUFFIX@">5</token> <import>macro_output.xml</import> <import>macro_test_output.xml</import> </macros> @@ -48,6 +48,7 @@ --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0} #if $model_preset == 'multimer': --multimer +--max-sequences \${ALPHAFOLD_MAX_SEQUENCES:-10} #end if > alphafold.fasta |
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| diff -r e4a053d67e24 -r 2f7702fd0a4c scripts/validate_fasta.py --- a/scripts/validate_fasta.py Fri Sep 01 00:09:46 2023 +0000 +++ b/scripts/validate_fasta.py Wed May 08 06:26:55 2024 +0000 |
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| @@ -5,7 +5,7 @@ import sys from typing import List -MULTIMER_MAX_SEQUENCE_COUNT = 10 +DEFAULT_MAX_SEQUENCE_COUNT = 10 STRIP_SEQUENCE_CHARS = ['\n', '\r', '\t', ' '] @@ -77,10 +77,12 @@ class FastaValidator: def __init__( - self, - min_length=None, - max_length=None, - multiple=False): + self, + min_length=None, + max_length=None, + multiple=False, + max_sequence_count=None, + ): self.multiple = multiple self.min_length = min_length self.max_length = max_length @@ -90,6 +92,9 @@ 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', '-' } + self.max_sequence_count = ( + max_sequence_count + or DEFAULT_MAX_SEQUENCE_COUNT) def validate(self, fasta_list: List[Fasta]): """Perform FASTA validation.""" @@ -114,14 +119,11 @@ f' Only {fasta_count} sequences were detected in' ' the provided file.') - elif fasta_count > MULTIMER_MAX_SEQUENCE_COUNT: - sys.stderr.write( + elif fasta_count > self.max_sequence_count: + raise ValueError( f'WARNING: detected {fasta_count} sequences but the' - f' maximum allowed is {MULTIMER_MAX_SEQUENCE_COUNT}' - ' sequences. The last' - f' {fasta_count - MULTIMER_MAX_SEQUENCE_COUNT} sequence(s)' - ' have been discarded.\n') - self.fasta_list = self.fasta_list[:MULTIMER_MAX_SEQUENCE_COUNT] + f' maximum allowed is {self.max_sequence_count}' + ' sequences.') else: if fasta_count > 1: sys.stderr.write( @@ -200,6 +202,7 @@ min_length=args.min_length, max_length=args.max_length, multiple=args.multimer, + max_sequence_count=args.max_sequence_count, ) clean_fastas = fv.validate(fas.fastas) @@ -246,6 +249,13 @@ type=int, ) parser.add_argument( + "--max-sequences", + dest='max_sequence_count', + help="Maximum number of input sequences", + default=None, + type=int, + ) + parser.add_argument( "--multimer", action='store_true', help="Require multiple input sequences", |