Mercurial > repos > iuc > medaka_consensus_pipeline

annotate macros.xml @ 17:d9b6a4615626 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
author iuc
date Tue, 28 Oct 2025 09:58:19 +0000
parents fc8804320156
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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1 <macros>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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2 <token name="@TOOL_VERSION@">2.1.1</token>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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3 <token name="@VERSION_SUFFIX@">0</token>
14
cb34f00cc10f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 8051b858e0f5c6d7c1092754df02ed8303a53054
iuc
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4 <token name="@PROFILE@">21.01</token>
11
8dfe8a52346f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
iuc
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5 <xml name="bio_tools">
8dfe8a52346f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
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6 <xrefs>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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7 <xref type="bio.tools">medaka</xref>
11
8dfe8a52346f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
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8 </xrefs>
8dfe8a52346f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
iuc
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9 </xml>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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10 <xml name="requirements">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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11 <requirements>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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12 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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13 <requirement type="package" version="1.16.2">scipy</requirement>
4
a1b70f038b4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
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14 <yield />
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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15 </requirements>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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16 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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17 <xml name="version_command">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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18 <version_command>medaka --version</version_command>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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19 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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20 <xml name="citations">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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21 <citations>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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22 <citation type="bibtex">@online{medaka,
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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23 author = {Oxford Nanopore Technologies Ltd.},
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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24 title = {medaka},
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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25 year = 2020,
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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26 url = {https://github.com/nanoporetech/medaka},
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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27 urldate = {2020-05-06}
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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28 }</citation>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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29 </citations>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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30 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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31
1
551f8c9bc4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
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32 <!--
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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33 command
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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34 -->
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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35
1
551f8c9bc4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
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36 <token name="@REF_FASTA@"><![CDATA[
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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37 #if $reference_source.reference_source_selector == 'history':
9
a7228a7ea146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
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38 #if $reference_source.ref_file.ext.endswith(".gz")
a7228a7ea146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
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39 gunzip -c '$reference_source.ref_file' > reference.fa &&
a7228a7ea146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
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40 #else
16
fc8804320156 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7105600c6ba7a49e8933e1a1357566fc2126df58
iuc
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41 cp '$reference_source.ref_file' reference.fa &&
9
a7228a7ea146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
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42 #end if
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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43 #else:
16
fc8804320156 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7105600c6ba7a49e8933e1a1357566fc2126df58
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44 cp '$reference_source.ref_file.fields.path' reference.fa &&
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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45 #end if
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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46 ]]></token>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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47
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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48 <!--
1
551f8c9bc4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
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49 input
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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50 -->
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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51
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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52 <xml name="b" token_argument="-b">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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53 <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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54 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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55 <xml name="model" token_argument="-m" token_label="Select model">
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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56 <param argument="@ARGUMENT@" type="select" label="@LABEL@" help="For best results it is important to specify the correct model,
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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57 according to the basecaller used. Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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58 or PromethION), iii) the basecaller variant, and iv) the basecaller version">
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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59 <option value="r103_fast_g507">r103_fast_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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60 <option value="r103_fast_snp_g507">r103_fast_snp_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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61 <option value="r103_fast_variant_g507">r103_fast_variant_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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62 <option value="r103_hac_g507">r103_hac_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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63 <option value="r103_hac_snp_g507">r103_hac_snp_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
64 <option value="r103_hac_variant_g507">r103_hac_variant_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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65 <option value="r103_sup_g507">r103_sup_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
66 <option value="r103_sup_snp_g507">r103_sup_snp_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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67 <option value="r103_sup_variant_g507">r103_sup_variant_g507</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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68 <option value="r1041_e82_260bps_fast_g632">r1041_e82_260bps_fast_g632</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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69 <option value="r1041_e82_260bps_fast_variant_g632">r1041_e82_260bps_fast_variant_g632</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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70 <option value="r1041_e82_260bps_hac_g632">r1041_e82_260bps_hac_g632</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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71 <option value="r1041_e82_260bps_hac_v4.0.0">r1041_e82_260bps_hac_v4.0.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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72 <option value="r1041_e82_260bps_hac_v4.1.0">r1041_e82_260bps_hac_v4.1.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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73 <option value="r1041_e82_260bps_hac_variant_g632">r1041_e82_260bps_hac_variant_g632</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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74 <option value="r1041_e82_260bps_hac_variant_v4.1.0">r1041_e82_260bps_hac_variant_v4.1.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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75 <option value="r1041_e82_260bps_joint_apk_ulk_v5.0.0">r1041_e82_260bps_joint_apk_ulk_v5.0.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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76 <option value="r1041_e82_260bps_sup_g632">r1041_e82_260bps_sup_g632</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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77 <option value="r1041_e82_260bps_sup_v4.0.0">r1041_e82_260bps_sup_v4.0.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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78 <option value="r1041_e82_260bps_sup_v4.1.0">r1041_e82_260bps_sup_v4.1.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
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79 <option value="r1041_e82_260bps_sup_variant_g632">r1041_e82_260bps_sup_variant_g632</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
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diff changeset
80 <option value="r1041_e82_260bps_sup_variant_v4.1.0">r1041_e82_260bps_sup_variant_v4.1.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
81 <option value="r1041_e82_400bps_bacterial_methylation">r1041_e82_400bps_bacterial_methylation</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
82 <option value="r1041_e82_400bps_fast_g615">r1041_e82_400bps_fast_g615</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
83 <option value="r1041_e82_400bps_fast_g632">r1041_e82_400bps_fast_g632</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
84 <option value="r1041_e82_400bps_fast_variant_g615">r1041_e82_400bps_fast_variant_g615</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
85 <option value="r1041_e82_400bps_fast_variant_g632">r1041_e82_400bps_fast_variant_g632</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
86 <option value="r1041_e82_400bps_hac_g615">r1041_e82_400bps_hac_g615</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
87 <option value="r1041_e82_400bps_hac_g632">r1041_e82_400bps_hac_g632</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
88 <option value="r1041_e82_400bps_hac_v4.0.0">r1041_e82_400bps_hac_v4.0.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
89 <option value="r1041_e82_400bps_hac_v4.1.0">r1041_e82_400bps_hac_v4.1.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
90 <option value="r1041_e82_400bps_hac_v4.2.0">r1041_e82_400bps_hac_v4.2.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
91 <option value="r1041_e82_400bps_hac_v4.3.0">r1041_e82_400bps_hac_v4.3.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
92 <option value="r1041_e82_400bps_hac_v5.0.0">r1041_e82_400bps_hac_v5.0.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
93 <option value="r1041_e82_400bps_hac_v5.0.0_rl_lstm384_dwells">r1041_e82_400bps_hac_v5.0.0_rl_lstm384_dwells</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
94 <option value="r1041_e82_400bps_hac_v5.0.0_rl_lstm384_no_dwells">r1041_e82_400bps_hac_v5.0.0_rl_lstm384_no_dwells</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
95 <option value="r1041_e82_400bps_hac_v5.2.0">r1041_e82_400bps_hac_v5.2.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
96 <option value="r1041_e82_400bps_hac_v5.2.0_rl_lstm384_dwells">r1041_e82_400bps_hac_v5.2.0_rl_lstm384_dwells</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
97 <option value="r1041_e82_400bps_hac_v5.2.0_rl_lstm384_no_dwells">r1041_e82_400bps_hac_v5.2.0_rl_lstm384_no_dwells</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
98 <option value="r1041_e82_400bps_hac_variant_g615">r1041_e82_400bps_hac_variant_g615</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
99 <option value="r1041_e82_400bps_hac_variant_g632">r1041_e82_400bps_hac_variant_g632</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
100 <option value="r1041_e82_400bps_hac_variant_v4.1.0">r1041_e82_400bps_hac_variant_v4.1.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
101 <option value="r1041_e82_400bps_hac_variant_v4.2.0">r1041_e82_400bps_hac_variant_v4.2.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
102 <option value="r1041_e82_400bps_hac_variant_v4.3.0">r1041_e82_400bps_hac_variant_v4.3.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
103 <option value="r1041_e82_400bps_hac_variant_v5.0.0">r1041_e82_400bps_hac_variant_v5.0.0</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
104 <option value="r1041_e82_400bps_sup_g615">r1041_e82_400bps_sup_g615</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
105 <option value="r1041_e82_400bps_sup_v4.0.0">r1041_e82_400bps_sup_v4.0.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
106 <option value="r1041_e82_400bps_sup_v4.1.0">r1041_e82_400bps_sup_v4.1.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
107 <option value="r1041_e82_400bps_sup_v4.2.0">r1041_e82_400bps_sup_v4.2.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
108 <option value="r1041_e82_400bps_sup_v4.3.0">r1041_e82_400bps_sup_v4.3.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
109 <option value="r1041_e82_400bps_sup_v5.0.0">r1041_e82_400bps_sup_v5.0.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
110 <option value="r1041_e82_400bps_sup_v5.0.0_rl_lstm384_dwells">r1041_e82_400bps_sup_v5.0.0_rl_lstm384_dwells</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
111 <option value="r1041_e82_400bps_sup_v5.0.0_rl_lstm384_no_dwells">r1041_e82_400bps_sup_v5.0.0_rl_lstm384_no_dwells</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
112 <option value="r1041_e82_400bps_sup_v5.2.0">r1041_e82_400bps_sup_v5.2.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
113 <option value="r1041_e82_400bps_sup_v5.2.0_rl_lstm384_dwells">r1041_e82_400bps_sup_v5.2.0_rl_lstm384_dwells</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
114 <option value="r1041_e82_400bps_sup_v5.2.0_rl_lstm384_no_dwells">r1041_e82_400bps_sup_v5.2.0_rl_lstm384_no_dwells</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
115 <option value="r1041_e82_400bps_sup_variant_g615">r1041_e82_400bps_sup_variant_g615</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
116 <option value="r1041_e82_400bps_sup_variant_v4.1.0">r1041_e82_400bps_sup_variant_v4.1.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
117 <option value="r1041_e82_400bps_sup_variant_v4.2.0">r1041_e82_400bps_sup_variant_v4.2.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
118 <option value="r1041_e82_400bps_sup_variant_v4.3.0">r1041_e82_400bps_sup_variant_v4.3.0</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
119 <option value="r1041_e82_400bps_sup_variant_v5.0.0">r1041_e82_400bps_sup_variant_v5.0.0</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
120 <option value="r104_e81_fast_g5015">r104_e81_fast_g5015</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
121 <option value="r104_e81_fast_variant_g5015">r104_e81_fast_variant_g5015</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
122 <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
123 <option value="r104_e81_hac_variant_g5015">r104_e81_hac_variant_g5015</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
124 <option value="r104_e81_sup_g5015">r104_e81_sup_g5015</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
125 <option value="r104_e81_sup_g610">r104_e81_sup_g610</option>
17
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
126 <option value="r104_e81_sup_variant_g610">r104_e81_sup_variant_g610</option>
d9b6a4615626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
iuc
parents: 16
diff changeset
127 <option value="r941_e81_fast_g514">r941_e81_fast_g514</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
128 <option value="r941_e81_fast_variant_g514">r941_e81_fast_variant_g514</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
129 <option value="r941_e81_hac_g514">r941_e81_hac_g514</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
130 <option value="r941_e81_hac_variant_g514">r941_e81_hac_variant_g514</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
131 <option value="r941_e81_sup_g514">r941_e81_sup_g514</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
132 <option value="r941_e81_sup_variant_g514">r941_e81_sup_variant_g514</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
133 <option value="r941_min_fast_g507">r941_min_fast_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
134 <option value="r941_min_fast_snp_g507">r941_min_fast_snp_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
135 <option value="r941_min_fast_variant_g507">r941_min_fast_variant_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
136 <option value="r941_min_hac_g507">r941_min_hac_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
137 <option value="r941_min_hac_snp_g507">r941_min_hac_snp_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
138 <option value="r941_min_hac_variant_g507">r941_min_hac_variant_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
139 <option value="r941_min_sup_g507">r941_min_sup_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
140 <option value="r941_min_sup_snp_g507">r941_min_sup_snp_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
141 <option value="r941_min_sup_variant_g507">r941_min_sup_variant_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
142 <option value="r941_prom_fast_g507">r941_prom_fast_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
143 <option value="r941_prom_fast_snp_g507">r941_prom_fast_snp_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
144 <option value="r941_prom_fast_variant_g507">r941_prom_fast_variant_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
145 <option value="r941_prom_hac_g507">r941_prom_hac_g507</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
146 <option value="r941_prom_hac_snp_g507">r941_prom_hac_snp_g507</option>
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147 <option value="r941_prom_hac_variant_g507">r941_prom_hac_variant_g507</option>
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148 <option value="r941_prom_sup_g507">r941_prom_sup_g507</option>
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149 <option value="r941_prom_sup_snp_g507">r941_prom_sup_snp_g507</option>
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150 <option value="r941_prom_sup_variant_g507">r941_prom_sup_variant_g507</option>
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151 <option value="r941_sup_plant_g610">r941_sup_plant_g610</option>
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152 <option value="r941_sup_plant_variant_g610">r941_sup_plant_variant_g610</option>
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153 </param>
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154 </xml>
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155 <xml name="reference">
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156 <conditional name="reference_source">
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157 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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158 <option value="cached">Use a built-in genome</option>
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159 <option value="history">Use a genome from history</option>
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160 </param>
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161 <when value="cached">
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162 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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163 <options from_data_table="all_fasta">
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164 <filter type="sort_by" column="2"/>
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165 <validator type="no_options" message="No reference genomes are available"/>
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166 </options>
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167 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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168 </param>
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169 </when>
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170 <when value="history">
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171 <param name="ref_file" type="data" format="fasta,fasta.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
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172 </when>
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173 </conditional>
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174 </xml>
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175
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176 <!--
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177 Help
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178 -->
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179
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180 <token name="@WID@"><![CDATA[
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181 *medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.
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182
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183 This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
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184 ]]></token>
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185
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186 <token name="@MODELS@"><![CDATA[
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187
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188 ----
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189
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190 .. class:: infomark
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191
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192 **Models**
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193
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194 For best results it is important to specify the correct model, -m in the above, according to the basecaller used. Allowed values can be found by running medaka tools list\_models.
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195
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196 Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION or PromethION), iii) the basecaller variant, and iv) the basecaller version, with the format:
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197
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198 ::
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199
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200 {pore}_{device}_{caller variant}_{caller version}
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201
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202 For example the model named r941_min_fast_g303 should be used with data from MinION (or GridION) R9.4.1 flowcells using the fast Guppy basecaller version 3.0.3. By contrast the model
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203 r941_prom_hac_g303 should be used with PromethION data and the high accuracy basecaller (termed "hac" in Guppy configuration files). Where a version of Guppy has been used without an exactly corresponding medaka model, the medaka model with the highest version equal to or less than the guppy version should be selected.
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204
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205 ]]></token>
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206
0
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207 <token name="@REFERENCES@"><![CDATA[
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208 More information are available in the `github <https://github.com/nanoporetech/medaka>`_.
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209 ]]></token>
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210 </macros>