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galaxy/test/functional/tools/bibtex.xml
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<tool id="bibtex" name="bibtex" version="0.1.0" license="AFL-3.0">
<creator>
<person
givenName="Björn"
familyName="Grüning"
url="https://github.com/bgruening"
identifier="http://orcid.org/0000-0002-3079-6586" />
<organization
url="https://galaxyproject.org/iuc/"
name="Galaxy IUC" />
</creator>
<xrefs>
<xref type="bio.tools">Citation.js</xref>
</xrefs>
<command><![CDATA[
echo '$input1' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="integer" help="integer" value="8" />
</inputs>
<outputs>
<data name="out_file1" format="txt" />
</outputs>
<tests>
</tests>
<help><![CDATA[
.. class:: warningmark
**WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
]]></help>
<citations>
<citation type="doi">10.1101/gr.4086505</citation>
<citation type="doi">10.6084/m9.figshare.979190</citation>
<citation type="bibtex">
@misc{Garrison2015,
author = {Garrison, Erik},
year = {2015},
title = {vcflib},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/ekg/vcflib},
}
</citation>
<citation type="bibtex">
@online{lh32017,
author = {Heng Li},
year = {2017},
title = {bwa},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/lh3/bwa},
}
</citation>
<!-- BibTeX examples taken from:
http://www2.galcit.caltech.edu/~jeshep/GraphicsBib/NatBib/node3.html
-->
<citation type="bibtex">
@ARTICLE{article-minimal,
author = {L[eslie] A. Aamport},
title = {The Gnats and Gnus Document Preparation System},
journal = {\mbox{G-Animal's} Journal},
year = 1986,
}
</citation>
<citation type="bibtex">
@ARTICLE{article-full,
author = {L[eslie] A. Aamport},
title = {The Gnats and Gnus Document Preparation System},
journal = {\mbox{G-Animal's} Journal},
year = 1986,
volume = 41,
number = 7,
pages = "73+",
month = jul,
note = "This is a full ARTICLE entry",
}
</citation>
<citation type="bibtex">
@INBOOK{inbook-minimal,
author = "Donald E. Knuth",
title = "Fundamental Algorithms",
publisher = "Addison-Wesley",
year = "{\noopsort{1973b}}1973",
chapter = "1.2",
}
</citation>
<citation type="bibtex">
@INBOOK{inbook-full,
author = "Donald E. Knuth",
title = "Fundamental Algorithms",
volume = 1,
series = "The Art of Computer Programming",
publisher = "Addison-Wesley",
address = "Reading, Massachusetts",
edition = "Second",
month = "10~" # jan,
year = "{\noopsort{1973b}}1973",
type = "Section",
chapter = "1.2",
pages = "10--119",
note = "This is a full INBOOK entry",
}
</citation>
<citation type="bibtex">
@BOOK{book-minimal,
author = "Donald E. Knuth",
title = "Seminumerical Algorithms",
publisher = "Addison-Wesley",
year = "{\noopsort{1973c}}1981",
}
</citation>
<citation type="bibtex">
@BOOK{book-full,
author = "Donald E. Knuth",
title = "Seminumerical Algorithms",
volume = 2,
series = "The Art of Computer Programming",
publisher = "Addison-Wesley",
address = "Reading, Massachusetts",
edition = "Second",
month = "10~" # jan,
year = "{\noopsort{1973c}}1981",
note = "This is a full BOOK entry",
}
</citation>
<citation type="bibtex">
@BOOK{whole-set,
author = "Donald E. Knuth",
publisher = "Addison-Wesley",
title = "The Art of Computer Programming",
series = "Four volumes",
year = "{\noopsort{1973a}}{\switchargs{--90}{1968}}",
note = "Seven volumes planned (this is a cross-referenced set of BOOKs)",
}
</citation>
<citation type="bibtex">
@BOOKLET{booklet-full,
author = "Jill C. Knvth",
title = "The Programming of Computer Art",
howpublished = "Vernier Art Center",
address = "Stanford, California",
month = feb,
year = 1988,
note = "This is a full BOOKLET entry",
}
</citation>
<citation type="bibtex">
@INCOLLECTION{incollection-minimal,
author = "Daniel D. Lincoll",
title = "Semigroups of Recurrences",
booktitle = "High Speed Computer and Algorithm Organization",
publisher = "Academic Press",
year = 1977,
}
</citation>
<citation type="bibtex">
@INCOLLECTION{incollection-full,
author = "Daniel D. Lincoll",
title = "Semigroups of Recurrences",
editor = "David J. Lipcoll and D. H. Lawrie and A. H. Sameh",
booktitle = "High Speed Computer and Algorithm Organization",
number = 23,
series = "Fast Computers",
chapter = 3,
type = "Part",
pages = "179--183",
publisher = "Academic Press",
address = "New York",
edition = "Third",
month = sep,
year = 1977,
note = "This is a full INCOLLECTION entry",
}
</citation>
<citation type="bibtex">
@BOOK{whole-collection,
editor = "David J. Lipcoll and D. H. Lawrie and A. H. Sameh",
title = "High Speed Computer and Algorithm Organization",
booktitle = "High Speed Computer and Algorithm Organization",
number = 23,
series = "Fast Computers",
publisher = "Academic Press",
address = "New York",
edition = "Third",
month = sep,
year = 1977,
}
</citation>
<citation type="bibtex">
@MANUAL{manual-full,
author = "Larry Manmaker",
title = "The Definitive Computer Manual",
organization = "Chips-R-Us",
address = "Silicon Valley",
edition = "Silver",
month = apr # "-" # may,
year = 1986,
note = "This is a full MANUAL entry",
}
</citation>
<citation type="bibtex">
@MASTERSTHESIS{mastersthesis-minimal,
author = "{\'{E}}douard Masterly",
title = "Mastering Thesis Writing",
school = "Stanford University",
year = 1988,
}
</citation>
<citation type="bibtex">
@MASTERSTHESIS{mastersthesis-full,
author = "{\'{E}}douard Masterly",
title = "Mastering Thesis Writing",
school = "Stanford University",
type = "Master's project",
address = "English Department",
month = jun # "-" # aug,
year = 1988,
note = "This is a full MASTERSTHESIS entry",
}
</citation>
<citation type="bibtex">
@MISC{misc-full,
author = "Joe-Bob Missilany",
title = "Handing out random pamphlets in airports",
howpublished = "Handed out at O'Hare",
month = oct,
year = 1984,
note = "This is a full MISC entry",
}
</citation>
<citation type="bibtex">
@INPROCEEDINGS{inproceedings-minimal,
author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis",
title = "On Notions of Information Transfer in {VLSI} Circuits",
booktitle = "Proc. Fifteenth Annual ACM" # STOC,
year = 1983,
}
</citation>
<citation type="bibtex">
@INPROCEEDINGS{inproceedings-full,
author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis",
title = "On Notions of Information Transfer in {VLSI} Circuits",
editor = "Wizard V. Oz and Mihalis Yannakakis",
booktitle = "Proc. Fifteenth Annual ACM" # STOC,
number = 17,
series = "All ACM Conferences",
pages = "133--139",
month = mar,
year = 1983,
address = "Boston",
organization = ACM,
publisher = "Academic Press",
note = "This is a full INPROCEDINGS entry",
}
</citation>
<citation type="bibtex">
@INPROCEEDINGS{inproceedings-crossref,
crossref = "whole-proceedings",
author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis",
title = "On Notions of Information Transfer in {VLSI} Circuits",
organization = "",
pages = "133--139",
note = "This is a cross-referencing INPROCEEDINGS entry",
}
</citation>
<citation type="bibtex">
@PROCEEDINGS{proceedings-full,
editor = "Wizard V. Oz and Mihalis Yannakakis",
title = "Proc. Fifteenth Annual" # STOC,
number = 17,
series = "All ACM Conferences",
month = mar,
year = 1983,
address = "Boston",
organization = ACM,
publisher = "Academic Press",
note = "This is a full PROCEEDINGS entry",
}
</citation>
<citation type="bibtex">
@PHDTHESIS{phdthesis-minimal,
author = "F. Phidias Phony-Baloney",
title = "Fighting Fire with Fire: Festooning {F}rench Phrases",
school = "Fanstord University",
year = 1988,
}
</citation>
<citation type="bibtex">
@PHDTHESIS{phdthesis-full,
author = "F. Phidias Phony-Baloney",
title = "Fighting Fire with Fire: Festooning {F}rench Phrases",
school = "Fanstord University",
type = "{PhD} Dissertation",
address = "Department of French",
month = jun # "-" # aug,
year = 1988,
note = "This is a full PHDTHESIS entry",
}
</citation>
<citation type="bibtex">
@TECHREPORT{techreport-minimal,
author = "Tom Terrific",
title = "An {$O(n \log n / \! \log\log n)$} Sorting Algorithm",
institution = "Fanstord University",
year = 1988,
}
</citation>
<citation type="bibtex">
@TECHREPORT{techreport-full,
author = "Tom T{\'{e}}rrific",
title = "An {$O(n \log n / \! \log\log n)$} Sorting Algorithm",
institution = "Fanstord University",
type = "Wishful Research Result",
number = "7",
address = "Computer Science Department, Fanstord, California",
month = oct,
year = 1988,
note = "This is a full TECHREPORT entry",
}
</citation>
<citation type="bibtex">
@UNPUBLISHED{unpublished-minimal,
author = "Ulrich {\"{U}}nderwood and Ned {\~N}et and Paul {\={P}}ot",
title = "Lower Bounds for Wishful Research Results",
note = "Talk at Fanstord University (this is a minimal UNPUBLISHED entry)",
}
</citation>
<citation type="bibtex">
@UNPUBLISHED{unpublished-full,
author = "Ulrich {\"{U}}nderwood and Ned {\~N}et and Paul {\={P}}ot",
title = "Lower Bounds for Wishful Research Results",
month = nov # ", " # dec,
year = 1988,
note = "Talk at Fanstord University (this is a full UNPUBLISHED entry)",
}
</citation>
</citations>
</tool>
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