| Previous changeset 3:e95d3221b7f0 (2020-09-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 6aeacd9ee8abb962fd7037cc374598caa87e63b3" |
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modified:
iedb_api.py iedb_api.xml test-data/seqs.fa test-data/seqs.tsv |
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| diff -r e95d3221b7f0 -r 7ed6dda64a81 iedb_api.py --- a/iedb_api.py Fri Sep 11 21:02:34 2020 +0000 +++ b/iedb_api.py Sat Feb 13 00:06:36 2021 +0000 |
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| @@ -73,8 +73,21 @@ if length is not None: if prediction == 'bcell': params['window_size'] = str(length).encode() + elif length == 'asis': + params['length'] = str(length).encode() else: - params['length'] = str(length).encode() + slen = len(seq) + alleles = [] + lengths = [] + for i in zip(length.split(','), allele.split(',')): + if int(i[0]) <= slen: + lengths.append(i[0]) + alleles.append(i[1]) + if lengths: + params['length'] = str(','.join(lengths)).encode() + params['allele'] = str(','.join(alleles)).encode() + else: + return results req_data = urlencode(params) if debug: print('url %s %s' % (url, unquote(req_data)), file=sys.stderr) |
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| diff -r e95d3221b7f0 -r 7ed6dda64a81 iedb_api.xml --- a/iedb_api.xml Fri Sep 11 21:02:34 2020 +0000 +++ b/iedb_api.xml Sat Feb 13 00:06:36 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="iedb_api" name="IEDB" version="2.15.1"> +<tool id="iedb_api" name="IEDB" version="2.15.2"> <description>MHC Binding prediction</description> <macros> <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples=""> @@ -13,7 +13,7 @@ </param> </when> <when value="entry"> - <param name="allele_text" type="text" size="80" label="Alleles"> + <param name="allele_text" type="text" label="Alleles"> <help>Enter alleles separated by white space: @HLA_EXAMPLES@ (The peptide lengths may follow each allele: @HLALEN_EXAMPLES@)</help> <validator type="regex" message="Doesn't appear to be a valid allele">^@HLA_REGEX@(\s+@HLA_REGEX@)*$</validator> </param> |
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| diff -r e95d3221b7f0 -r 7ed6dda64a81 test-data/seqs.fa --- a/test-data/seqs.fa Fri Sep 11 21:02:34 2020 +0000 +++ b/test-data/seqs.fa Sat Feb 13 00:06:36 2021 +0000 |
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| @@ -2,3 +2,5 @@ GHAHKVPRRLLKAAR >peptide2 LKAADASADADGSGSGSGSG +>peptide3 +KDLGYDYS |
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| diff -r e95d3221b7f0 -r 7ed6dda64a81 test-data/seqs.tsv --- a/test-data/seqs.tsv Fri Sep 11 21:02:34 2020 +0000 +++ b/test-data/seqs.tsv Sat Feb 13 00:06:36 2021 +0000 |
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| @@ -1,2 +1,3 @@ peptide1 16 GHAHKVPRRLLKAAR peptide2 21 LKAADASADADGSGSGSGSG +peptide3 8 KDLGYDYS |