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annotate complexity_fasta.xml @ 8:9def47f3c1e4 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
author nml
date Tue, 06 Aug 2019 08:50:28 -0400
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9def47f3c1e4 planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
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1 <tool id="complexity_fasta" name="Complexity FASTA" version="0.7.0">
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2 <requirements>
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3 <requirement type="package" version="0.7.0">quasitools</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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7 quasitools complexity fasta '$input_fasta' -o output.csv
9def47f3c1e4 planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
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9def47f3c1e4 planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
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9 ]]></command>
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10 <inputs>
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11 <param name="input_fasta" type="data" format="fasta" optional="false" label="input file" />
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12 </inputs>
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13 <outputs>
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14 <data format="csv" name="output" from_work_dir="output.csv" />
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="input_fasta" value="msa.fasta" />
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19 <output name="output">
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20 <assert_contents>
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21 <has_text text="Number of Haplotypes" />
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22 <has_text text="8" />
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23 <has_text text="0.75" />
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24 </assert_contents>
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25 </output>
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26 </test>
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27 </tests>
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29 <help><![CDATA[
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30 Quasispecies Complexity
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31 =======================
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33 Measure the complexity of quasispecies reads using a variety of measures. The input must be an aligned FASTA file, representing a particular reqion of quasispcies from which to measure the complexity.
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35 The measures of complexity are taken from the following work:
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37 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
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40 ]]></help>
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41 <citations>
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42 <citation type="bibtex">
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43 @misc{GitHubquasitoolscomplexity,
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44 title = {quasitools complexity},
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45 publisher = {phac-nml},
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46 journal = {GitHub repository},
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47 url = {https://github.com/phac-nml/quasitools},
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48 }
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49 </citation>
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50 </citations>
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51 </tool>