Mercurial > repos > iuc > medaka_consensus_pipeline

annotate macros.xml @ 16:fc8804320156 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/master/tools/medaka commit 7105600c6ba7a49e8933e1a1357566fc2126df58
author iuc
date Tue, 26 Sep 2023 10:11:13 +0000
parents 79e9a869f40e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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1 <macros>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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2 <token name="@TOOL_VERSION@">1.7.2</token>
16
fc8804320156 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7105600c6ba7a49e8933e1a1357566fc2126df58
iuc
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3 <token name="@VERSION_SUFFIX@">1</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>
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8dfe8a52346f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
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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>
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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"
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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"
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12 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
4
a1b70f038b4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
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13 <yield />
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ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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14 </requirements>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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15 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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16 <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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17 <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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18 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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19 <xml name="citations">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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20 <citations>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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21 <citation type="bibtex">@online{medaka,
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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22 author = {Oxford Nanopore Technologies Ltd.},
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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23 title = {medaka},
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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24 year = 2020,
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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25 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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26 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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27 }</citation>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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28 </citations>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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29 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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30
1
551f8c9bc4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
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31 <!--
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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32 command
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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33 -->
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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34
1
551f8c9bc4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
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35 <token name="@REF_FASTA@"><![CDATA[
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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36 #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"
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37 #if $reference_source.ref_file.ext.endswith(".gz")
a7228a7ea146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
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38 gunzip -c '$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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39 #else
16
fc8804320156 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7105600c6ba7a49e8933e1a1357566fc2126df58
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40 cp '$reference_source.ref_file' reference.fa &&
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a7228a7ea146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
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41 #end if
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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42 #else:
16
fc8804320156 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7105600c6ba7a49e8933e1a1357566fc2126df58
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43 cp '$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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44 #end if
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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45 ]]></token>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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46
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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47 <!--
1
551f8c9bc4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
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48 input
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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49 -->
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 <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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52 <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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53 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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54 <xml name="model" token_argument="-m" token_label="Select model">
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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55 <param argument="@ARGUMENT@" type="select" label="@LABEL@" help="For best results it is important to specify the correct model,
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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56 according to the basecaller used. Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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57 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"
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58 <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"
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59 <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"
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60 <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"
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61 <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"
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62 <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
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63 <option value="r103_hac_variant_g507">r103_hac_variant_g507</option>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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64 <option value="r103_min_high_g345">r103_min_high_g345</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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65 <option value="r103_min_high_g360">r103_min_high_g360</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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66 <option value="r103_prom_high_g360">r103_prom_high_g360</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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67 <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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68 <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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69 <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
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70 <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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71 <option value="r103_sup_variant_g507">r103_sup_variant_g507</option>
15
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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72 <option value="r1041_e82_400bps_fast_g615">r1041_e82_400bps_fast_g615</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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73 <option value="r1041_e82_400bps_fast_variant_g615">r1041_e82_400bps_fast_variant_g615</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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74 <option value="r1041_e82_400bps_hac_g615">r1041_e82_400bps_hac_g615</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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75 <option value="r1041_e82_400bps_hac_variant_g615">r1041_e82_400bps_hac_variant_g615</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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76 <option value="r1041_e82_400bps_sup_g615">r1041_e82_400bps_sup_g615</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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77 <option value="r1041_e82_400bps_sup_variant_g615">r1041_e82_400bps_sup_variant_g615</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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78 <option value="r104_e81_fast_g5015">r104_e81_fast_g5015</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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79 <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option>
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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80 <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
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parents: 14
diff changeset
81 <option value="r104_e81_fast_variant_g5015">r104_e81_fast_variant_g5015</option>
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="r104_e81_hac_variant_g5015">r104_e81_hac_variant_g5015</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
83 <option value="r104_e81_sup_g610">r104_e81_sup_g610</option>
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="r104_e81_sup_variant_g610">r104_e81_sup_variant_g610</option>
10
1ca4ce7241fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
85 <option value="r10_min_high_g303">r10_min_high_g303</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="r10_min_high_g340">r10_min_high_g340</option>
79e9a869f40e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents: 14
diff changeset
87 <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
88 <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
89 <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
90 <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
91 <option value="r941_e81_sup_variant_g514">r941_e81_sup_variant_g514</option>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
92 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
93 <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
94 <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
95 <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
96 <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
97 <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
98 <option value="r941_min_hac_variant_g507">r941_min_hac_variant_g507</option>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
99 <option value="r941_min_high_g303">r941_min_high_g303</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
100 <option value="r941_min_high_g330">r941_min_high_g330</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
101 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
102 <option value="r941_min_high_g344">r941_min_high_g344</option>
2
6a87478ed985 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"
iuc
parents: 1
diff changeset
103 <option value="r941_min_high_g351">r941_min_high_g351</option>
10
1ca4ce7241fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
104 <option value="r941_min_high_g360" selected="true">r941_min_high_g360</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
105 <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
106 <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
107 <option value="r941_min_sup_variant_g507">r941_min_sup_variant_g507</option>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
108 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
109 <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
110 <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
111 <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
112 <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
113 <option value="r941_prom_hac_snp_g507">r941_prom_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
114 <option value="r941_prom_hac_variant_g507">r941_prom_hac_variant_g507</option>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
115 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
116 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
117 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
10
1ca4ce7241fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
118 <option value="r941_prom_high_g360">r941_prom_high_g360</option>
1ca4ce7241fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
119 <option value="r941_prom_high_g4011">r941_prom_high_g4011</option>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
120 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
121 <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
10
1ca4ce7241fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
122 <option value="r941_prom_snp_g360">r941_prom_snp_g360</option>
13
72b5e9dda577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 11
diff changeset
123 <option value="r941_prom_sup_g507">r941_prom_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
124 <option value="r941_prom_sup_snp_g507">r941_prom_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
125 <option value="r941_prom_sup_variant_g507">r941_prom_sup_variant_g507</option>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
126 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
127 <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
10
1ca4ce7241fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
128 <option value="r941_prom_variant_g360">r941_prom_variant_g360</option>
15
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_sup_plant_g610">r941_sup_plant_g610</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_sup_plant_variant_g610">r941_sup_plant_variant_g610</option>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
131 </param>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
132 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
133 <xml name="reference">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
134 <conditional name="reference_source">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
135 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
136 <option value="cached">Use a built-in genome</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
137 <option value="history">Use a genome from history</option>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
138 </param>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
139 <when value="cached">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
140 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
141 <options from_data_table="all_fasta">
2
6a87478ed985 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"
iuc
parents: 1
diff changeset
142 <filter type="sort_by" column="2"/>
6a87478ed985 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"
iuc
parents: 1
diff changeset
143 <validator type="no_options" message="No reference genomes are available"/>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
144 </options>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
145 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
146 </param>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
147 </when>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
148 <when value="history">
9
a7228a7ea146 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
parents: 4
diff changeset
149 <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"/>
0
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
150 </when>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
151 </conditional>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
152 </xml>
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
153
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
154 <!--
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
155 Help
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
156 -->
ef94bace3a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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157
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158 <token name="@WID@"><![CDATA[
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159 *medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.
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161 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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162 ]]></token>
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164 <token name="@MODELS@"><![CDATA[
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166 ----
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168 .. class:: infomark
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170 **Models**
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172 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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174 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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176 ::
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178 {pore}_{device}_{caller variant}_{caller version}
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180 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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181 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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183 ]]></token>
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184
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185 <token name="@REFERENCES@"><![CDATA[
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186 More information are available in the `manual <https://github.com/nanoporetech/medaka/tree/master/docs>`_ and `github <https://github.com/nanoporetech/medaka>`_.
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187 ]]></token>
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188 </macros>