Mercurial > repos > iuc > medaka_snp

annotate macros.xml @ 0:179342c7b86c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
author iuc
date Wed, 12 Oct 2022 07:43:59 +0000
parents
children 630e6aeeb7e8
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0
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
1 <macros>
179342c7b86c 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>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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3 <token name="@VERSION_SUFFIX@">0</token>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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4 <token name="@PROFILE@">21.01</token>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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5 <xml name="bio_tools">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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6 <xrefs>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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7 <xref type="bio.tools">medaka</xref>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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8 </xrefs>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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9 </xml>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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10 <xml name="requirements">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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11 <requirements>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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12 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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13 <yield />
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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14 </requirements>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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15 </xml>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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16 <xml name="version_command">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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17 <version_command>medaka --version</version_command>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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18 </xml>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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19 <xml name="citations">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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20 <citations>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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21 <citation type="bibtex">@online{medaka,
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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22 author = {Oxford Nanopore Technologies Ltd.},
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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23 title = {medaka},
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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24 year = 2020,
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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25 url = {https://github.com/nanoporetech/medaka},
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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26 urldate = {2020-05-06}
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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27 }</citation>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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28 </citations>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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29 </xml>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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30
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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31 <!--
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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32 command
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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33 -->
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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34
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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35 <token name="@REF_FASTA@"><![CDATA[
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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36 #if $reference_source.reference_source_selector == 'history':
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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37 #if $reference_source.ref_file.ext.endswith(".gz")
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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38 gunzip -c '$reference_source.ref_file' > reference.fa &&
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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39 #else
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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40 ln -f -s '$reference_source.ref_file' reference.fa &&
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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41 #end if
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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42 #else:
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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43 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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44 #end if
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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45 ]]></token>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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46
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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47 <!--
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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48 input
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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49 -->
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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50
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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51 <xml name="b" token_argument="-b">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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52 <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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53 </xml>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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54 <xml name="model" token_argument="-m" token_label="Select model">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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55 <param argument="@ARGUMENT@" type="select" label="@LABEL@" help="For best results it is important to specify the correct model,
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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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
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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57 or PromethION), iii) the basecaller variant, and iv) the basecaller version">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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58 <option value="r103_fast_g507">r103_fast_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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59 <option value="r103_fast_snp_g507">r103_fast_snp_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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60 <option value="r103_fast_variant_g507">r103_fast_variant_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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61 <option value="r103_hac_g507">r103_hac_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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62 <option value="r103_hac_snp_g507">r103_hac_snp_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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63 <option value="r103_hac_variant_g507">r103_hac_variant_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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64 <option value="r103_min_high_g345">r103_min_high_g345</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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65 <option value="r103_min_high_g360">r103_min_high_g360</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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66 <option value="r103_prom_high_g360">r103_prom_high_g360</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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67 <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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68 <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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69 <option value="r103_sup_g507">r103_sup_g507</option>
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70 <option value="r103_sup_snp_g507">r103_sup_snp_g507</option>
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71 <option value="r103_sup_variant_g507">r103_sup_variant_g507</option>
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72 <option value="r1041_e82_400bps_fast_g615">r1041_e82_400bps_fast_g615</option>
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73 <option value="r1041_e82_400bps_fast_variant_g615">r1041_e82_400bps_fast_variant_g615</option>
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74 <option value="r1041_e82_400bps_hac_g615">r1041_e82_400bps_hac_g615</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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75 <option value="r1041_e82_400bps_hac_variant_g615">r1041_e82_400bps_hac_variant_g615</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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76 <option value="r1041_e82_400bps_sup_g615">r1041_e82_400bps_sup_g615</option>
179342c7b86c 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>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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78 <option value="r104_e81_fast_g5015">r104_e81_fast_g5015</option>
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79 <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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80 <option value="r104_e81_sup_g5015">r104_e81_sup_g5015</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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81 <option value="r104_e81_fast_variant_g5015">r104_e81_fast_variant_g5015</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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82 <option value="r104_e81_hac_variant_g5015">r104_e81_hac_variant_g5015</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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83 <option value="r104_e81_sup_g610">r104_e81_sup_g610</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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diff changeset
84 <option value="r104_e81_sup_variant_g610">r104_e81_sup_variant_g610</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
85 <option value="r10_min_high_g303">r10_min_high_g303</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
86 <option value="r10_min_high_g340">r10_min_high_g340</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
87 <option value="r941_e81_fast_variant_g514">r941_e81_fast_variant_g514</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
88 <option value="r941_e81_hac_g514">r941_e81_hac_g514</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
89 <option value="r941_e81_hac_variant_g514">r941_e81_hac_variant_g514</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
90 <option value="r941_e81_sup_g514">r941_e81_sup_g514</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
91 <option value="r941_e81_sup_variant_g514">r941_e81_sup_variant_g514</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
92 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
93 <option value="r941_min_fast_g507">r941_min_fast_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
94 <option value="r941_min_fast_snp_g507">r941_min_fast_snp_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
95 <option value="r941_min_fast_variant_g507">r941_min_fast_variant_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
96 <option value="r941_min_hac_g507">r941_min_hac_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
97 <option value="r941_min_hac_snp_g507">r941_min_hac_snp_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
98 <option value="r941_min_hac_variant_g507">r941_min_hac_variant_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
99 <option value="r941_min_high_g303">r941_min_high_g303</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
100 <option value="r941_min_high_g330">r941_min_high_g330</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
101 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
102 <option value="r941_min_high_g344">r941_min_high_g344</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
103 <option value="r941_min_high_g351">r941_min_high_g351</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
104 <option value="r941_min_high_g360" selected="true">r941_min_high_g360</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
105 <option value="r941_min_sup_g507">r941_min_sup_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
106 <option value="r941_min_sup_snp_g507">r941_min_sup_snp_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
107 <option value="r941_min_sup_variant_g507">r941_min_sup_variant_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
108 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
109 <option value="r941_prom_fast_g507">r941_prom_fast_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
110 <option value="r941_prom_fast_snp_g507">r941_prom_fast_snp_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
111 <option value="r941_prom_fast_variant_g507">r941_prom_fast_variant_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
112 <option value="r941_prom_hac_g507">r941_prom_hac_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
113 <option value="r941_prom_hac_snp_g507">r941_prom_hac_snp_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
114 <option value="r941_prom_hac_variant_g507">r941_prom_hac_variant_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
115 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
116 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
117 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
118 <option value="r941_prom_high_g360">r941_prom_high_g360</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
119 <option value="r941_prom_high_g4011">r941_prom_high_g4011</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
120 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
121 <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
122 <option value="r941_prom_snp_g360">r941_prom_snp_g360</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
123 <option value="r941_prom_sup_g507">r941_prom_sup_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
124 <option value="r941_prom_sup_snp_g507">r941_prom_sup_snp_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
125 <option value="r941_prom_sup_variant_g507">r941_prom_sup_variant_g507</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
126 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
127 <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
128 <option value="r941_prom_variant_g360">r941_prom_variant_g360</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
129 <option value="r941_sup_plant_g610">r941_sup_plant_g610</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
130 <option value="r941_sup_plant_variant_g610">r941_sup_plant_variant_g610</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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diff changeset
131 </param>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
132 </xml>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
133 <xml name="reference">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
134 <conditional name="reference_source">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
135 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
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136 <option value="cached">Use a built-in genome</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
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137 <option value="history">Use a genome from history</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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138 </param>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
139 <when value="cached">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
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140 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
141 <options from_data_table="all_fasta">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
142 <filter type="sort_by" column="2"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
143 <validator type="no_options" message="No reference genomes are available"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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diff changeset
144 </options>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
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145 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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146 </param>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
147 </when>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
148 <when value="history">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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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"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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150 </when>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
151 </conditional>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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152 </xml>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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153
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
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154 <!--
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
155 Help
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
156 -->
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
157
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
158 <token name="@WID@"><![CDATA[
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
159 *medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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160
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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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.
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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diff changeset
162 ]]></token>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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163
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
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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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179
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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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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>