Mercurial > repos > dfornika > chewbbaca_schemaevaluator

annotate chewbbaca_schemaevaluator.xml @ 0:6053ca7c24f3 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
author dfornika
date Fri, 24 Jan 2020 19:33:33 +0000
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children 5037f1f7423c
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6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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1 <tool id="chewbbaca_schemaevaluator" name="chewBBACA SchemaEvaluator" version="@TOOL_VERSION@+galaxy0">
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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2 <description>BSR-Based Allele Calling Algorithm</description>
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3 <requirements>
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4 <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement>
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 chewBBACA.py SchemaEvaluator
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8 --cpu \${GALAXY_SLOTS:-1}
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9 -i '${schema}'
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10 -t '${threshold}'
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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11 ]]>
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12 </command>
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13 <inputs>
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14
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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15 </inputs>
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16
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17 <!-- define outputs -->
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18 <outputs>
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19 <data format="tabular" name="statistics" label="${tool.name}: on ${on_string}: Statistics" />
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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20 <data format="tabular" name="contigs_info" label="${tool.name}: on ${on_string}: Contigs Info" />
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21 <data format="tabular" name="alleles" label="${tool.name}: on ${on_string}: Alleles" />
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22 <data format="txt" name="log" label="${tool.name}: on ${on_string}: Log" />
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23 <data format="tabular" name="repeated_loci" label="${tool.name}: on ${on_string}: Repeated Loci" />
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24 </outputs>
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25 <tests>
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26
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27 </tests>
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28 <help><![CDATA[
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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29 ]]>
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30 </help>
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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31 <citations>
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32 <citation type="bibtex">
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33 @ARTICLE{andrews_s,
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34 author = {Rossi, M and Silva, M and Ribeiro-Gonçalves, B and Silva, DN
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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35 and Machado, MP and Oleastro, M and Borges, V and Isidro, J
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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36 and Gomes, JP and Vieira, L and Barker, DOR and Llarena, AK
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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37 and Halkilahti, J and Jaakkonen, A and Palma, F and Culebro, A
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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38 and Kivistö, R and Hänninen, ML and Laukkanen-Ninios, R
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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39 and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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40 and Garaizer, J and Bikandi, J and Hilbert, F and Taboada, EN
6053ca7c24f3 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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41 and Carriço, JA},
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42 keywords = {bioinformatics, ngs, mlst},
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43 title = {{INNUENDO whole and core genome MLST databases and schemas
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44 for foodborne pathogens}},
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45 url = {https://github.com/TheInnuendoProject/chewBBACA_schemas}
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46 }
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47 </citation>
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48 <citation type="doi">10.1099/mgen.0.000166</citation>
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49 <citation type="doi">10.1371/journal.pgen.1007261</citation>
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50 </citations>
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51 </tool>