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
line wrap: on
line diff
--- /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>')