# HG changeset patch
# User iuc
# Date 1647988208 0
# Node ID 91efba463050587f5fd5a635bc13173b5171d975
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
diff -r 000000000000 -r 91efba463050 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Tue Mar 22 22:30:08 2022 +0000
@@ -0,0 +1,17 @@
+Galaxy NCBI Entrez Direct Tools
+===============================
+
+This repo requires a readme as administrators should very aware of some
+restrictions NCBI places on the use of the Entrez service.
+
+NCBI requests that you please limit large jobs to either weekends or
+between 9:00 PM and 5:00 AM Eastern time during weekdays. This is not a
+request that the Galaxy tool can easily service, so we've included it in
+the disclaimer on every tool quite prominently.
+
+Failure to comply with NCBI's policies may result in an block.
+
+Note that these are *IP* level blocks so the Galaxy tools uses a
+concatenation of the administrator's emails, and the user email, in
+hopes that NCBI will contact all relevant parties should their system be
+abused.
diff -r 000000000000 -r 91efba463050 __efetch_build_options.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/__efetch_build_options.py Tue Mar 22 22:30:08 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 = '''pubmed
+protein
+nuccore
+nucleotide
+nucgss
+nucest
+structure
+genome
+annotinfo
+assembly
+bioproject
+biosample
+blastdbinfo
+books
+cdd
+clinvar
+clone
+gap
+gapplus
+grasp
+dbvar
+gene
+gds
+geoprofiles
+homologene
+medgen
+mesh
+ncbisearch
+nlmcatalog
+omim
+orgtrack
+pmc
+popset
+probe
+proteinclusters
+pcassay
+biosystems
+pccompound
+pcsubstance
+pubmedhealth
+seqannot
+snp
+sra
+taxonomy
+unigene
+gencoll
+gtr'''.replace("", "").replace("", "").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('')
+print(' ')
+for name in sorted(db.keys()):
+ if name == all:
+ continue
+ print(' ' % (name, name))
+print(' ')
+print(' ')
+
+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(' ' % name)
+ print(' ')
+ print(' ')
+ for format in sorted(my_dict.keys()):
+ print(' ' % (format, format or "None"))
+ print(' ')
+ for format in sorted(my_dict.keys()):
+ print(' ' % format)
+ print(' ')
+ if "" not in my_dict[format]:
+ my_dict[format].append("")
+ for mode in sorted(my_dict[format]):
+ print(' ' % (mode, mode or "None"))
+ print(' ')
+ print(' ')
+ print(' ')
+ print(' ')
+print(' ')
+print(' ')
+print(' ')
+print(' ')
+print(' ')
+print('')
diff -r 000000000000 -r 91efba463050 efetch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/efetch.xml Tue Mar 22 22:30:08 2022 +0000
@@ -0,0 +1,2581 @@
+
+ fetch records from NCBI
+
+ macros.xml
+
+
+ efetch -version
+ '${output_result}'
+ ]]>
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diff -r 000000000000 -r 91efba463050 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Mar 22 22:30:08 2022 +0000
@@ -0,0 +1,102 @@
+
+ 13.3
+
+
+ entrez-direct
+
+
+ /dev/null ;
+ ]]>
+
+ `__ is available on
+their website
+
+Liability
+~~~~~~~~~
+
+For documents and software available from this server, the
+U.S. Government does not warrant or assume any legal liability or
+responsibility for the accuracy, completeness, or usefulness of any
+information, apparatus, product, or process disclosed.
+
+Endorsement
+~~~~~~~~~~~
+
+NCBI does not endorse or recommend any commercial
+products, processes, or services. The views and opinions of authors
+expressed on NCBI's Web sites do not necessarily state or reflect those
+of the U.S. Government, and they may not be used for advertising or
+product endorsement purposes.
+
+External Links
+~~~~~~~~~~~~~~
+
+Some NCBI Web pages may provide links to other Internet
+sites for the convenience of users. NCBI is not responsible for the
+availability or content of these external sites, nor does NCBI endorse,
+warrant, or guarantee the products, services, or information described
+or offered at these other Internet sites. Users cannot assume that the
+external sites will abide by the same Privacy Policy to which NCBI
+adheres. It is the responsibility of the user to examine the copyright
+and licensing restrictions of linked pages and to secure all necessary
+permissions.
+ ]]>
+
+
+ @Book{ncbiEDirect,
+ author = {Jonathan Kans},
+ title = {Entrez Direct: E-utilities on the UNIX Command Line},
+ year = {2013},
+ publisher = {National Center for Biotechnology Information, Bethesda, Maryland},
+ note = {http://www.ncbi.nlm.nih.gov/books/NBK179288/}
+ }
+
+
+