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annotate complexity.xml @ 6:9fb9fed71486 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
author nml
date Fri, 12 Oct 2018 09:16:03 -0400
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9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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1 <tool id="complexity" name="Complexity" version="0.5.0">
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2 <description>measures the complexity of the quasispecies reads</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.0">quasitools</requirement>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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8 quasitools complexity $input_fasta > complexity.txt
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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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="Aligned FASTA Input" />
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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13 </inputs>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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14 <outputs>
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15 <data format="txt" label="Complexity" name="output_complexity" from_work_dir="complexity.txt" />
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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16 </outputs>
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9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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18 <tests>
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19 <test>
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20 <param name="input_fasta" value="msa.fasta" />
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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21 <output name="output_complexity">
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22 <assert_contents>
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23 <has_text text="Number of haplotypes (H) : 8" />
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24 <has_text text="Mutation Frequency (Mfe) : 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.
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36 The measures of complexity are taken from the following work:
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
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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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42 <citations>
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43 </citations>
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44 </tool>