Mercurial > repos > iuc > ncbi_entrez_direct_esearch
diff __efetch_build_options.py @ 0:b6ffd64c448e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
| author | iuc |
|---|---|
| date | Tue, 22 Mar 2022 22:30:57 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/__efetch_build_options.py Tue Mar 22 22:30:57 2022 +0000 @@ -0,0 +1,225 @@ +#!/usr/bin/env python + +# Daniel Blankenberg +# Creates the options for tool interface + +# http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi +db_list = '''<DbName>pubmed</DbName> +<DbName>protein</DbName> +<DbName>nuccore</DbName> +<DbName>nucleotide</DbName> +<DbName>nucgss</DbName> +<DbName>nucest</DbName> +<DbName>structure</DbName> +<DbName>genome</DbName> +<DbName>annotinfo</DbName> +<DbName>assembly</DbName> +<DbName>bioproject</DbName> +<DbName>biosample</DbName> +<DbName>blastdbinfo</DbName> +<DbName>books</DbName> +<DbName>cdd</DbName> +<DbName>clinvar</DbName> +<DbName>clone</DbName> +<DbName>gap</DbName> +<DbName>gapplus</DbName> +<DbName>grasp</DbName> +<DbName>dbvar</DbName> +<DbName>gene</DbName> +<DbName>gds</DbName> +<DbName>geoprofiles</DbName> +<DbName>homologene</DbName> +<DbName>medgen</DbName> +<DbName>mesh</DbName> +<DbName>ncbisearch</DbName> +<DbName>nlmcatalog</DbName> +<DbName>omim</DbName> +<DbName>orgtrack</DbName> +<DbName>pmc</DbName> +<DbName>popset</DbName> +<DbName>probe</DbName> +<DbName>proteinclusters</DbName> +<DbName>pcassay</DbName> +<DbName>biosystems</DbName> +<DbName>pccompound</DbName> +<DbName>pcsubstance</DbName> +<DbName>pubmedhealth</DbName> +<DbName>seqannot</DbName> +<DbName>snp</DbName> +<DbName>sra</DbName> +<DbName>taxonomy</DbName> +<DbName>unigene</DbName> +<DbName>gencoll</DbName> +<DbName>gtr</DbName>'''.replace("<DbName>", "").replace("</DbName>", "").split("\n") + + +help = ''' (all) + docsum DocumentSummarySet XML + docsum json DocumentSummarySet JSON + full Same as native except for mesh + uid Unique Identifier List + url Entrez URL + xml Same as -format full -mode xml + + bioproject + native BioProject Report + native xml RecordSet XML + + biosample + native BioSample Report + native xml BioSampleSet XML + + biosystems + native xml Sys-set XML + + gds + native xml RecordSet XML + summary Summary + + gene + gene_table Gene Table + native Gene Report + native asn.1 Entrezgene ASN.1 + native xml Entrezgene-Set XML + tabular Tabular Report + + homologene + alignmentscores Alignment Scores + fasta FASTA + homologene Homologene Report + native Homologene List + native asn.1 HG-Entry ASN.1 + native xml Entrez-Homologene-Set XML + + mesh + full Full Record + native MeSH Report + native xml RecordSet XML + + nlmcatalog + native Full Record + native xml NLMCatalogRecordSet XML + + pmc + medline MEDLINE + native xml pmc-articleset XML + + pubmed + abstract Abstract + medline MEDLINE + native asn.1 Pubmed-entry ASN.1 + native xml PubmedArticleSet XML + + (sequences) + acc Accession Number + est EST Report + fasta FASTA + fasta xml TinySeq XML + fasta_cds_aa FASTA of CDS Products + fasta_cds_na FASTA of Coding Regions + ft Feature Table + gb GenBank Flatfile + gb xml GBSet XML + gbc xml INSDSet XML + gbwithparts GenBank with Contig Sequences + gene_fasta FASTA of Gene + gp GenPept Flatfile + gp xml GBSet XML + gpc xml INSDSet XML + gss GSS Report + ipg Identical Protein Report + ipg xml IPGReportSet XML + native text Seq-entry ASN.1 + native xml Bioseq-set XML + seqid Seq-id ASN.1 + + snp + chr Chromosome Report + docset Summary + fasta FASTA + flt Flat File + native asn.1 Rs ASN.1 + native xml ExchangeSet XML + rsr RS Cluster Report + ssexemplar SS Exemplar List + + sra + native xml EXPERIMENT_PACKAGE_SET XML + runinfo xml SraRunInfo XML + + structure + mmdb Ncbi-mime-asn1 strucseq ASN.1 + native MMDB Report + native xml RecordSet XML + + taxonomy + native Taxonomy List + native xml TaxaSet XML'''.split("\n") + +db = {} +name = None +all = "(all)" +for line in help: + if line.strip() and line[2] != ' ': + name = line.strip() + db[name] = {} + elif line.strip(): + format = line[0:len(" docsum ")].strip() + mode = line[len(" docsum "):len(" docsum json ")].strip() + if format not in db[name]: + db[name][format] = [] + db[name][format].append(mode) + +for name in db_list: + if name not in db: + db[name] = {} + +db["sequences"] = db["(sequences)"] +del db["(sequences)"] + +print('<conditional name="db">') +print(' <param name="db" type="select" label="Database" argument="-db">') +for name in sorted(db.keys()): + if name == all: + continue + print(' <option value="%s">%s</option>' % (name, name)) +print(' <option value="">Manual Entry</option>') +print(' </param>') + +for name in sorted(db.keys()): + if name == all: + continue + my_dict = db[all].copy() + + for format, modes in db[name].items(): + if format in my_dict: + for mode in modes: + if mode not in my_dict[format]: + my_dict[format].append(mode) + else: + my_dict[format] = modes + if "" not in my_dict: + my_dict[""] = [""] + print(' <when value="%s">' % name) + print(' <conditional name="format">') + print(' <param name="format" type="select" label="Format" argument="-format">') + for format in sorted(my_dict.keys()): + print(' <option value="%s">%s</option>' % (format, format or "None")) + print(' </param>') + for format in sorted(my_dict.keys()): + print(' <when value="%s">' % format) + print(' <param name="mode" type="select" label="Mode" argument="-mode">') + if "" not in my_dict[format]: + my_dict[format].append("") + for mode in sorted(my_dict[format]): + print(' <option value="%s">%s</option>' % (mode, mode or "None")) + print(' </param>') + print(' </when>') + print(' </conditional>') + print(' </when>') +print(' <when value="">') +print(' <param name="db_manual" type="text" label="Database" argument="-db"/>') +print(' <param name="format" type="text" label="Format" argument="-format"/>') +print(' <param name="mode" type="text" label="Mode" argument="-mode"/>') +print(' </when>') +print('</conditional>')