Mercurial > repos > iuc > medaka_consensus

annotate macros.xml @ 13:fa11aa8103b2 draft

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 86211daa63a6f39524df8759364795b782324303"
author iuc
date Fri, 17 Sep 2021 20:22:04 +0000
parents 9f70e869f61e
children b2aae698b9d3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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diff changeset
1 <?xml version="1.0"?>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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2 <macros>
11
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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3 <token name="@TOOL_VERSION@">1.3.2</token>
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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4 <token name="@PROFILE@">20.01</token>
12
9f70e869f61e "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">
9f70e869f61e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
iuc
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6 <xrefs>
9f70e869f61e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
iuc
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7 <xref type="bio.tools">khmer</xref>
9f70e869f61e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
iuc
parents: 11
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8 </xrefs>
9f70e869f61e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
iuc
parents: 11
diff changeset
9 </xml>
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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10 <xml name="requirements">
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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11 <requirements>
0632744d5a5f "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>
5
5901bb391198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
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13 <yield />
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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14 </requirements>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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15 </xml>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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16 <xml name="version_command">
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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17 <version_command>medaka --version</version_command>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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18 </xml>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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19 <xml name="citations">
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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20 <citations>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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21 <citation type="bibtex">@online{medaka,
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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22 author = {Oxford Nanopore Technologies Ltd.},
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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23 title = {medaka},
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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24 year = 2020,
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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25 url = {https://github.com/nanoporetech/medaka},
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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26 urldate = {2020-05-06}
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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27 }</citation>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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28 </citations>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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29 </xml>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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30
2
12c40c8c86db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 1
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31 <!--
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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32 command
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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33 -->
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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34
2
12c40c8c86db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 1
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35 <token name="@REF_FASTA@"><![CDATA[
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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36 #if $reference_source.reference_source_selector == 'history':
10
db25ec99c3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
parents: 5
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37 #if $reference_source.ref_file.ext.endswith(".gz")
db25ec99c3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
parents: 5
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38 gunzip -c '$reference_source.ref_file' > reference.fa &&
db25ec99c3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
parents: 5
diff changeset
39 #else
db25ec99c3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
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40 ln -f -s '$reference_source.ref_file' reference.fa &&
db25ec99c3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
iuc
parents: 5
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41 #end if
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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42 #else:
2
12c40c8c86db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 1
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43 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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44 #end if
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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45 ]]></token>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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46
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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47 <!--
2
12c40c8c86db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 1
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48 input
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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49 -->
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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50
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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51 <xml name="b" token_argument="-b">
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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52 <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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53 </xml>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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54 <xml name="model" token_argument="-m" token_label="Select model">
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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55 <param argument="@ARGUMENT@" type="select" label="@LABEL@">
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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56 <option value="r103_min_high_g345">r103_min_high_g345</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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57 <option value="r103_min_high_g360">r103_min_high_g360</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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58 <option value="r103_prom_high_g360">r103_prom_high_g360</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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59 <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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60 <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
11
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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61 <option value="r10_min_high_g303">r10_min_high_g303</option>
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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62 <option value="r10_min_high_g340">r10_min_high_g340</option>
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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63 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
64 <option value="r941_min_high_g303">r941_min_high_g303</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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65 <option value="r941_min_high_g330">r941_min_high_g330</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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66 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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67 <option value="r941_min_high_g344">r941_min_high_g344</option>
3
a95960a63220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"
iuc
parents: 2
diff changeset
68 <option value="r941_min_high_g351">r941_min_high_g351</option>
11
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 10
diff changeset
69 <option value="r941_min_high_g360" selected="true">r941_min_high_g360</option>
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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70 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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71 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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72 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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73 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
11
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 10
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74 <option value="r941_prom_high_g360">r941_prom_high_g360</option>
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 10
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75 <option value="r941_prom_high_g4011">r941_prom_high_g4011</option>
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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76 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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77 <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
11
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 10
diff changeset
78 <option value="r941_prom_snp_g360">r941_prom_snp_g360</option>
1
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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79 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
0632744d5a5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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80 <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
11
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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81 <option value="r941_prom_variant_g360">r941_prom_variant_g360</option>
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82 </param>
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83 </xml>
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84 <xml name="reference">
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85 <conditional name="reference_source">
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86 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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87 <option value="cached">Use a built-in genome</option>
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88 <option value="history">Use a genome from history</option>
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89 </param>
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90 <when value="cached">
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91 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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92 <options from_data_table="all_fasta">
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93 <filter type="sort_by" column="2"/>
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94 <validator type="no_options" message="No reference genomes are available"/>
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95 </options>
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96 <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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97 </param>
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98 </when>
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99 <when value="history">
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100 <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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101 </when>
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102 </conditional>
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103 </xml>
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104
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105 <!--
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106 Help
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107 -->
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108
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109 <token name="@WID@"><![CDATA[
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110 *medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.
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111
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112 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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113 ]]></token>
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114 <token name="@REFERENCES@"><![CDATA[
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115 More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_.
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116 ]]></token>
12
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117 </macros>