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annotate complexity_fasta.xml @ 9:18aad692772a draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
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18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1 <tool id="complexity_fasta" name="Complexity FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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5 <expand macro="requirements"/>
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6 <command detect_errors="exit_code"><![CDATA[
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9def47f3c1e4 planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
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8 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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10 ]]></command>
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11 <inputs>
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12 <param name="input_fasta" type="data" format="fasta" optional="false" label="input file" />
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13 </inputs>
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14 <outputs>
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15 <data format="csv" name="output" from_work_dir="output.csv" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input_fasta" value="msa.fasta" />
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20 <output name="output">
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21 <assert_contents>
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22 <has_text text="Number of Haplotypes" />
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23 <has_text text="8" />
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24 <has_text text="0.75" />
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25 </assert_contents>
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26 </output>
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27 </test>
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28 </tests>
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30 <help><![CDATA[
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31 Quasispecies Complexity
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32 =======================
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34 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.
9def47f3c1e4 planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
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36 The measures of complexity are taken from the following work:
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38 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
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41 ]]></help>
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18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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42 <expand macro="citations" />
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43 </tool>