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annotate pangolin.xml @ 0:f612c8391bd8 draft

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"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
author nml
date Fri, 01 May 2020 11:30:48 -0400
parents
children b91b3923656e
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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1 <tool id="pangolon" name="Pangolin" version="@VERSION@+galaxy0">
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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2 <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</description>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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3 <macros>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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4 <import>macros.xml</import>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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5 </macros>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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6 <expand macro="requirements" />
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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7 <command detect_errors="exit_code"><![CDATA[
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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9 pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length'
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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11 ]]></command>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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12 <inputs>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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13 <param name="input1" type="data" format="fasta"
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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14 label="Input multi-sequence fasta file"
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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15 />
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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16 <section name="additional" title="Additional Parameters" expanded="false">
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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17 <param name="max_ambig" type="float" value="0.5" min="0" max="1.0"
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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18 label="Maximum proportion of Ns allowed to attempt assignment"
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19 argument="--max-ambig"
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20 />
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21 <param name="min_length" type="integer" value="10000" min="0"
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22 label="Minimum query length to attempt assignment"
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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23 argument="--min-length"
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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24 />
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25 </section>
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26 </inputs>
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27 <outputs>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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28 <data format="csv" from_work_dir="lineage_report.csv" name="lineage_report" label="${input1.name}_lineage_report" />
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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29 </outputs>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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30 <tests>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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31 <test>
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32 <param name="input1" value="test_seqs.fasta" />
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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33 <output name="lineage_report" value="lineage_report.csv" />
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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34 </test>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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35 </tests>
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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36 <help><![CDATA[
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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38 Pangolin
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39 --------
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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41 Pangolin assigns SARS-CoV-2 genome sequences in fasta format to global lineages from `Rambaut et al. <https://doi.org/10.1101/2020.04.17.046086>`_.
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42 To do this, Pangolin employs the use of external programs including: `iqtree <http://www.iqtree.org/#download>`_, `mafft <https://mafft.cbrc.jp/alignment/software/>`_,
f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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43 and `snakemake <https://snakemake.readthedocs.io/en/stable/index.html>`_.
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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45 More information can be obtained from the authors github site: https://github.com/hCoV-2019/pangolin
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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47 --------------
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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49 **Input** - Multi sequence fasta file
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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f612c8391bd8 "planemo upload for repository https://github.com/hCoV-2019/pangolin commit 5278814fe0175e7ac73ae3f43c443bbe549197ee"
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52 **Output** - lineage report:
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54 +---------+---------+------+-------------+------------------+-----------+-----------+
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55 | Taxon | Lineage | aLRT | UFbootstrap | lineages_version | status | note |
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56 +=========+=========+======+=============+==================+===========+===========+
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57 | Sample1 | A.1 | 100 | 60 | 2020-04-27 | passed_qc | |
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58 +---------+---------+------+-------------+------------------+-----------+-----------+
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59 | Sample2 | B.1 | 80 | 80 | 2020-04-27 | passed_qc | |
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60 +---------+---------+------+-------------+------------------+-----------+-----------+
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61 | Sample3 | B.1.4 | 60 | 100 | 2020-04-27 | fail | seq_len:0 |
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62 +---------+---------+------+-------------+------------------+-----------+-----------+
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65 Resources for interpreting aLRT and UFbootstrap values:
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67 - `IQ_TREE: Assessing branch supports with single branch tests <http://www.iqtree.org/doc/Tutorial#assessing-branch-supports-with-single-branch-tests>`_
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69 - `IQ_TREE: Command Reference <http://www.iqtree.org/doc/Command-Reference>`_
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71 ]]></help>
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72 <expand macro="citations" />
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73 </tool>