view macros.xml @ 6:3c50a937d7c1 draft

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<macros>
  <macro name="basic_errors">
    <exit_code range="1:" level="fatal"/>
    <regex match="error" level="fatal"/>
    <regex match="traceback" level="fatal"/>
    <regex match="warning" level="warning"/>
  </macro>
  <macro name="cite_seqmagick">
    <citation type="bibtex">@MISC{fhcrc_seqmagick,
  title       = {seqmagick: An imagemagick-like frontend to Biopython SeqIO},
  author      = {McCoy, C. O. and Hodges, B. and Rosenthal, C. and Gallagher, A. and Matsen, IV, F. A.},
  publisher   = {GitHub},
  url         = "http://github.com/fhcrc/seqmagick",
  note        = "version 0.5.0"
}
    </citation>
  </macro>
  <!-- Biopython 1.63 -->
  <macro name="cite_biopython">
    <citation type="doi">10.1093/bioinformatics/btp163</citation>
  </macro>
  <macro name="cite_taxtastic">
    <citation type="bibtex">@MISC{fhcrc_taxtastic,
  title       = {taxtastic: Create and maintain phylogenetic "reference packages" of biological sequences},
  author      = {McCoy, C. O. and Hoffman, N. G. and Gallagher, A. and Hodges, B. and Ross, F. and Matsen, IV, F. A.},
  publisher   = {GitHub},
  url         = "http://github.com/fhcrc/taxtastic",
  note        = "version 0.5.2"
}
    </citation>
  </macro>
  <!-- INFERNAL 1.1 -->
  <macro name="cite_infernal">
    <citation type="doi">10.1093/bioinformatics/btt509</citation>
  </macro>
  <!-- pplacer 1.1alpha
       (the citation is for pplacer 1.0) -->
  <macro name="cite_pplacer">
    <citation type="doi">10.1186/1471-2105-11-538</citation>
    <citation type="bibtex">@MISC{fhcrc_pplacer,
  title       = {pplacer: Phylogenetic placement and downstream analysis},
  author      = {Gallagher, A. and McCoy, C. O. and Claywell, B. C. and Small, C. T. and Hodges, B. and Hoffman, N. G. and Matsen, IV, F. A.},
  publisher   = {GitHub},
  url         = "http://github.com/matsen/pplacer",
  note        = "version v1.1.alpha16-1-gf748c91"
}
    </citation>
  </macro>
  <!-- USEARCH 6 -->
  <macro name="cite_usearch">
    <citation type="doi">10.1093/bioinformatics/btq461</citation>
  </macro>
</macros>