diff __efetch_build_options.py @ 0:18e6b25259ff draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/__efetch_build_options.py	Thu Jul 07 02:40:33 2016 -0400
@@ -0,0 +1,267 @@
+#!/usr/bin/env python
+# Daniel Blankenberg
+# Creates the options for tool interface
+import re
+
+# http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
+db_list = '''
+<DbName>annotinfo</DbName>
+<DbName>assembly</DbName>
+<DbName>bioproject</DbName>
+<DbName>biosample</DbName>
+<DbName>biosystems</DbName>
+<DbName>blastdbinfo</DbName>
+<DbName>books</DbName>
+<DbName>cdd</DbName>
+<DbName>clinvar</DbName>
+<DbName>clone</DbName>
+<DbName>dbvar</DbName>
+<DbName>gap</DbName>
+<DbName>gapplus</DbName>
+<DbName>gds</DbName>
+<DbName>gencoll</DbName>
+<DbName>gene</DbName>
+<DbName>genome</DbName>
+<DbName>geoprofiles</DbName>
+<DbName>grasp</DbName>
+<DbName>gtr</DbName>
+<DbName>homologene</DbName>
+<DbName>medgen</DbName>
+<DbName>mesh</DbName>
+<DbName>ncbisearch</DbName>
+<DbName>nlmcatalog</DbName>
+<DbName>nuccore</DbName>
+<DbName>nucest</DbName>
+<DbName>nucgss</DbName>
+<DbName>nucleotide</DbName>
+<DbName>omim</DbName>
+<DbName>orgtrack</DbName>
+<DbName>pcassay</DbName>
+<DbName>pccompound</DbName>
+<DbName>pcsubstance</DbName>
+<DbName>pmc</DbName>
+<DbName>popset</DbName>
+<DbName>probe</DbName>
+<DbName>protein</DbName>
+<DbName>proteinclusters</DbName>
+<DbName>pubmed</DbName>
+<DbName>pubmedhealth</DbName>
+<DbName>seqannot</DbName>
+<DbName>snp</DbName>
+<DbName>sra</DbName>
+<DbName>structure</DbName>
+<DbName>taxonomy</DbName>
+<DbName>unigene</DbName>'''.replace( "<DbName>", "").replace( "</DbName>", "").split("\n")
+
+
+help = '''  (all)
+                 docsum             xml      Document Summary
+                 docsum             json     Document Summary
+                 full               text     Full Document
+                 uilist             xml      Unique Identifier List
+                 uilist             text     Unique Identifier List
+                 full               xml      Full Document
+
+  bioproject
+                 native                      BioProject Report
+                 native             xml      RecordSet
+
+  biosample
+                 native                      BioSample Report
+                 native             xml      BioSampleSet
+
+  biosystems
+                 native             xml      Sys-set
+
+  gds
+                 native             xml      RecordSet
+                 summary            text     Summary
+
+  gene
+                 gene_table         xml      Gene Table
+                 native             text     Gene Report
+                 native             asn.1    Entrezgene
+                 native             xml      Entrezgene-Set
+                 tabular            tabular  Tabular Report
+
+  homologene
+                 alignmentscores    text     Alignment Scores
+                 fasta              fasta    FASTA
+                 homologene         text     Homologene Report
+                 native             text     Homologene List
+                 native             asn.1    HG-Entry
+                 native             xml      Entrez-Homologene-Set
+
+  mesh
+                 full               text     Full Record
+                 native             text     MeSH Report
+                 native             xml      RecordSet
+
+  nlmcatalog
+                 native             text     Full Record
+                 native             xml      NLMCatalogRecordSet
+
+  pmc
+                 medline            text     MEDLINE
+                 native             xml      pmc-articleset
+
+  pubmed
+                 abstract           xml      Abstract
+                 medline            text     MEDLINE
+                 native             asn.1    Pubmed-entry
+                 native             xml      PubmedArticleSet
+
+  (sequences)
+                 acc                text     Accession Number
+                 est                xml      EST Report
+                 fasta              fasta    FASTA
+                 fasta              xml      TinySeq
+                 fasta_cds_aa       fasta    CDS Products
+                 fasta_cds_na       fasta    Coding Regions
+                 ft                 text     Feature Table
+                 gb                 text     GenBank Flatfile
+                 gb                 xml      GBSet
+                 gbc                xml      INSDSet
+                 gbwithparts        text     GenBank with Contig Sequences
+                 gene_fasta         fasta    FASTA of Gene
+                 gp                 text     GenPept Flatfile
+                 gp                 xml      GBSet
+                 gpc                xml      INSDSet
+                 gss                text     GSS Report
+                 ipg                text     Identical Protein Report
+                 ipg                xml      IPGReportSet
+                 native             text     Seq-entry
+                 native             xml      Bioseq-set
+                 seqid              asn.1    Seq-id
+
+  snp
+                 chr                text     Chromosome Report
+                 docset             text     Summary
+                 fasta              fasta    FASTA
+                 flt                text     Flat File
+                 native             asn.1    Rs
+                 native             xml      ExchangeSet
+                 rsr                tabular  RS Cluster Report
+                 ssexemplar         text     SS Exemplar List
+
+  sra
+                 native             xml      EXPERIMENT_PACKAGE_SET
+                 runinfo            xml      SraRunInfo
+
+  structure
+                 mmdb               asn.1    Ncbi-mime-asn1 strucseq
+                 native             text     MMDB Report
+                 native             xml      RecordSet
+
+  taxonomy
+                 native             text     Taxonomy List
+                 native             xml      TaxaSet'''.split("\n")
+
+
+db = {}
+for db_name in db_list:
+    db[db_name] = []
+
+section = None
+for line in help:
+    line = re.split('\s{2,}', line.strip())
+    # Ignore empties
+    if len(line) == 0:
+        continue
+    # Section headers have one item
+    elif len(line) == 1:
+        section = line[0]
+        db[section] = []
+    # Format lines have 2+
+    elif len(line) == 2:
+        parent_format = line[0]
+        description = line[1]
+
+        if parent_format not in db[section]:
+            db[section].append((parent_format, None, description))
+    elif len(line) == 3:
+        parent_format = line[0]
+        format_modifier = line[1]
+        description = line[2]
+
+        if parent_format not in db[section]:
+            db[section].append((parent_format, format_modifier, description))
+
+
+all_formats = db['(all)']
+del db['(all)']
+sequences_formats = db['(sequences)']
+del db['(sequences)']
+del db['']
+
+for key in db:
+    db[key] += all_formats
+
+for key in ('nuccore', 'nucest', 'nucgss', 'nucleotide'):
+    db[key] += sequences_formats
+
+MACRO_TPL = '''
+
+'''
+
+WHEN_TPL = '''      <when value="{format}">
+        <param name="output_format" type="select" label="Output Format">
+          {format_options}
+        </param>
+      </when>'''
+
+FORMAT_OPTION_TPL = '''<option value="{name_type}">{name_type_human}</option>'''
+
+format_names = {}
+
+print '''  <xml name="db">
+    <conditional name="db">
+      <expand macro="dbselect" />'''
+for key in sorted(db):
+    format_options = []
+
+    for (parent_format, format_modifier, description) in sorted(db[key]):
+        name_human = description
+        if format_modifier:
+            name_human += ' (%s)' % format_modifier
+        format_string = '%s-%s' % (parent_format, format_modifier)
+
+        format_options.append(FORMAT_OPTION_TPL.format(
+            name_type=format_string,
+            name_type_human=name_human,
+        ))
+
+        format_names[format_string] = format_modifier
+
+    print WHEN_TPL.format(
+        format=key,
+        format_options='\n          '.join(format_options)
+    )
+
+print '''    </conditional>
+  </xml>'''
+
+CHANGE_FORMAT_TPL = '''
+  <xml name="efetch_formats">
+    <change_format>
+      {formats}
+    </change_format>
+  </xml>
+'''
+
+CHANGE_FORMAT_WHEN_TPL = '''<when input="output_format" value="{key}" format="{value}"/>'''
+# Format options
+
+
+whens = []
+for (k, v) in format_names.items():
+    if v is None:
+        v = 'text'
+    elif v == 'asn.1':
+        v = 'asn1'
+
+    whens.append(CHANGE_FORMAT_WHEN_TPL.format(
+        key=k, value=v
+    ))
+
+print CHANGE_FORMAT_TPL.format(formats='\n      '.join(whens))