Mercurial > repos > iuc > verkko

annotate verkko.xml @ 1:b70c923fb453 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 27c4b4ef34e34f9d7b29a2b94ebf8fbb69514626
author iuc
date Fri, 02 Jun 2023 03:55:52 +0000
parents b56a102fa59b
children
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b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
parents:
diff changeset
1 <tool id="verkko" name="verkko" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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2 <description>hybrid genome assembly pipeline</description>
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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3 <macros>
1
b70c923fb453 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 27c4b4ef34e34f9d7b29a2b94ebf8fbb69514626
iuc
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4 <token name="@TOOL_VERSION@">1.3.1</token>
b70c923fb453 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 27c4b4ef34e34f9d7b29a2b94ebf8fbb69514626
iuc
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5 <token name="@VERSION_SUFFIX@">0</token>
0
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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6 </macros>
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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7 <requirements>
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">verkko</requirement>
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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9 </requirements>
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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10 <command detect_errors="exit_code"><![CDATA[
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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11 #set $hififiles = []
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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12 #for $i, $datafile in enumerate($hifi):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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13 #set $filename_gz = str($i) + "_hifi.fastq.gz"
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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14 #set $filename = str($i) + "_hifi.fastq"
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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15 #if $datafile.is_of_type("fastq") or $datafile.is_of_type("fastqsanger"):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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16 ln -s '$datafile' '$filename' &&
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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17 #silent $hififiles.append($filename)
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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18 #else:
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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19 ln -s '$datafile' '$filename_gz' &&
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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20 #silent $hififiles.append($filename_gz)
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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21 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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22 #end for
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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23 #if $nano:
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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24 #set $nanofiles = []
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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25 #for $j, $ontfile in enumerate($nano):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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26 #set $filename_gz = str($j) + "_nano.fastq.gz"
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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27 #set $filename = str($j) + "_nano.fastq"
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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28 #if $ontfile.is_of_type("fastq") or $ontfile.is_of_type("fastqsanger"):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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29 ln -s '${ontfile}' '$filename' &&
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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30 #silent $nanofiles.append($filename)
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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31 #else:
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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32 ln -s '$ontfile' '$filename_gz' &&
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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33 #silent $nanofiles.append($filename_gz)
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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34 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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35 #end for
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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36 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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37 #if $algorithm.hap_kmer.hap_kmers == "yes":
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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38 mkdir 'h1.meryl' &&
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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39 tar -xzmf '$algorithm.hap_kmer.h1' -C 'h1.meryl' --strip-components 1 &&
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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40 mkdir h2.meryl &&
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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41 tar -xzmf '$algorithm.hap_kmer.h2' -C 'h2.meryl' --strip-components 1 &&
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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42 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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43 verkko --hifi
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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44 #for $k, $hifi_data in enumerate($hififiles):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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45 '$hifi_data'
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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46 #end for
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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47 #if $nano:
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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48 --nano
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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49 #for $k, $nano_data in enumerate($nanofiles):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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50 '$nano_data'
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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51 #end for
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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52 #else:
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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53 --no-nano
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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54 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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55 $algorithm.no_correction
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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56 #if $algorithm.hap_kmer.hap_kmers == "yes":
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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57 --hap-kmers 'h1.meryl' 'h2.meryl' $algorithm.hap_kmer.type
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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58 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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59 #if str($algorithm.base_k):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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60 --base-k $algorithm.base_k
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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61 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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62 #if str($algorithm.max_k):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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63 --max-k $algorithm.max_k
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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64 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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65 #if str($algorithm.window):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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66 --window $algorithm.window
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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67 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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68 #if str($algorithm.split_bases):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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69 --split-bases $algorithm.split_bases
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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70 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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71 #if str($algorithm.split_reads):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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72 --split-reads $algorithm.split_reads
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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73 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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74 #if str($algorithm.min_ont_length):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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75 --min-ont-length $algorithm.min_ont_length
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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76 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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77 #if str($algorithm.correct_k_mer_size):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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78 --correct-k-mer-size $algorithm.correct_k_mer_size
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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79 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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80 #if str($algorithm.correct_mer_threshold):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
iuc
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81 --correct-mer-threshold $algorithm.correct_mer_threshold
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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82 #end if
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83 #if str($algorithm.correct_min_read_length):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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84 --correct-min-read-length $algorithm.correct_min_read_length
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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85 #end if
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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86 #if str($algorithm.correct_min_overlap_length):
b56a102fa59b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141
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87 --correct-min-overlap-length $algorithm.correct_min_overlap_length
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88 #end if
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89 #if str($algorithm.correct_hash_bits):
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90 --correct-hash-bits $algorithm.correct_hash_bits
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91 #end if
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92 #if str($algorithm.seed_min_length):
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93 --seed-min-length $algorithm.seed_min_length
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94 #end if
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95 #if str($algorithm.seed_max_length):
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96 --seed-max-length $algorithm.seed_max_length
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97 #end if
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98 #if str($algorithm.align_bandwidth):
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99 --align-bandwidth $algorithm.align_bandwidth
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100 #end if
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101 #if str($algorithm.score_fraction):
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102 --score-fraction $algorithm.score_fraction
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103 #end if
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104 #if str($algorithm.min_identity):
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105 --min-identity $algorithm.min_identity
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106 #end if
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107 #if str($algorithm.min_score):
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108 --min-score $algorithm.min_score
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109 #end if
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110 #if str($algorithm.end_clipping):
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111 --end-clipping $algorithm.end_clipping
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112 #end if
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113 #if str($algorithm.incompatible_cutoff):
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114 --incompatible-cutoff $algorithm.incompatible_cutoff
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115 #end if
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116 -d asm
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117 ##This limits the amount of memory available to a given step 10 90% of maximum. This means 1 CPU,
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118 ##90% of max available memory, and max time 12 hrs for a given step
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119 --ovs-run 1 \$((\${GALAXY_MEMORY_MB:-8192} * 9 / 10)) 12
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120 ]]></command>
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121 <inputs>
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122 <param name="hifi" type="data" multiple="true" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="HiFi Reads Files" />
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123 <param name="nano" type="data" multiple="true" optional="true" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Oxford Nanopore Reads Files" />
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124 <section name="algorithm" title="Algorithm parameters">
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125 <param argument="--no-correction" type="boolean" truevalue="--no-correction" falsevalue="" label="Do not perform Canu correction on HiFi reads"/>
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126 <conditional name="hap_kmer">
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127 <param argument="--hap-kmers" type="select" label="Assign haplotypes from meryl databases">
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128 <option value="no">No</option>
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129 <option value="yes">Yes</option>
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130 </param>
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131 <when value="no"/>
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132 <when value="yes">
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133 <param name="h1" type="data" format="meryldb" label="h1"/>
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134 <param name="h2" type="data" format="meryldb" label="h2"/>
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135 <param name="type" type="select" label="Type">
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136 <option value="trio">Trio</option>
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137 <option value="hic">HiC</option>
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138 <option value="strandseq">Strandseq</option>
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139 </param>
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140 </when>
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141 </conditional>
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142 <param argument="--base-k" type="integer" label="Base k" min="0" optional="true"/>
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143 <param argument="--max-k" type="integer" label="Max k" min="0" optional="true"/>
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144 <param argument="--window" type="integer" label="Window" min="0" optional="true"/>
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145 <param argument="--split-bases" type="integer" label="Split bases" min="0" optional="true"/>
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146 <param argument="--split-reads" type="integer" label="Split reads" min="0" optional="true"/>
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147 <param argument="--min-ont-length" type="integer" label="Min ont length" min="0" optional="true"/>
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148 <param argument="--correct-k-mer-size" type="integer" label="Correct k mer size" min="0" optional="true"/>
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149 <param argument="--correct-mer-threshold" type="integer" label="Correct mer threshold" min="0" optional="true"/>
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150 <param argument="--correct-min-read-length" type="integer" label="Correct min read length" min="0" optional="true"/>
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151 <param argument="--correct-min-overlap-length" type="integer" label=" Correct min overlap length" min="0" optional="true"/>
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152 <param argument="--correct-hash-bits" type="integer" label="Correct hash bits" min="0" optional="true"/>
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153 <param argument="--seed-min-length" type="integer" label="Seed min length" min="0" optional="true"/>
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154 <param argument="--seed-max-length" type="integer" label="Seed max length" min="0" optional="true"/>
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155 <param argument="--align-bandwidth" type="integer" label="Align bandwidth" min="0" optional="true"/>
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156 <param argument="--score-fraction" type="float" label="Score fraction" min="0" optional="true"/>
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157 <param argument="--min-identity" type="float" label="Min identity" min="0" optional="true"/>
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158 <param argument="--min-score" type="integer" label="Min score" min="0" optional="true"/>
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159 <param argument="--end-clipping" type="integer" label="End clipping" min="0" optional="true"/>
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160 <param argument="--incompatible-cutoff" type="float" label="Incompatible cutoff" min="0" optional="true"/>
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161 </section>
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162 </inputs>
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163 <outputs>
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164 <!-- BASIC OUTFILES -->
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165 <data name="assembly_fasta" format="fasta" label="Verkko on ${on_string}: assembly fasta" from_work_dir="asm/assembly.fasta"/>
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166 <data name="hifi_coverage" format="tabular" label="Verkko on ${on_string}: hifi coverage" from_work_dir="asm/assembly.hifi-coverage.csv"/>
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167 <data name="homo_gfa" format="gfa1" label="Verkko on ${on_string}: Final graph" from_work_dir="asm/assembly.homopolymer-compressed.gfa"/>
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168 <data name="homo_layout" format="tabular" label="Verkko on ${on_string}: Homopolymer layout" from_work_dir="asm/assembly.homopolymer-compressed.layout"/>
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169 <data name="homo_noseq" format="gfa1" label="Verkko on ${on_string}: Homopolymer noseq" from_work_dir="asm/assembly.homopolymer-compressed.noseq.gfa"/>
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170 <data name="ont_coverage" format="tabular" label="Verkko on ${on_string}: ONT coverage" from_work_dir="asm/assembly.ont-coverage.csv"/>
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171 <data name="hifi_corrected" format="fasta.gz" label="Verkko on ${on_string}: Hifi corrected reads" from_work_dir="asm/hifi-corrected.fasta.gz">
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172 <filter>algorithm['no_correction'] == False</filter>
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173 </data>
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174 <!-- HAPLOTYPES OUT -->
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175 <data name="unassigned" format="fasta" label="Verkko on ${on_string}: Unassigned sequences" from_work_dir="asm/assembly.unassigned.fasta">
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176 <filter>algorithm['hap_kmer']['hap_kmers'] == "yes"</filter>
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177 </data>
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178 <data name="haplo_fasta_1" format="fasta" label="Verkko on ${on_string}: assembly haplotype fasta 1" from_work_dir="asm/assembly.haplotype1.fasta">
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179 <filter>algorithm['hap_kmer']['hap_kmers'] == "yes"</filter>
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180 </data>
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181 <data name="haplo_fasta_2" format="fasta" label="Verkko on ${on_string}: assembly haplotype fasta 2" from_work_dir="asm/assembly.haplotype2.fasta">
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182 <filter>algorithm['hap_kmer']['hap_kmers'] == "yes"</filter>
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183 </data>
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184 </outputs>
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185 <tests>
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186 <!-- ALL TESTS SHOULD FAIL, there is no sample data small enough to run in our tests, so it's checking the command itself -->
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187 <test expect_exit_code="1" expect_failure="true">
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188 <!-- Use nano, no haplotypes -->
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189 <param name="hifi" value="test1.fastq.gz,test2.fastq.gz"/>
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190 <param name="nano" value="test3.fastq.gz,test4.fastq.gz"/>
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191 <section name="algorithm">
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192 <param name="base_k" value="1003"/>
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193 <param name="max_k" value="15001"/>
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194 <param name="window" value="99"/>
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195 <param name="split_bases" value="3000000001"/>
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196 <param name="split_reads" value="150001"/>
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197 <param name="min_ont_length" value="2"/>
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198 <param name="correct_k_mer_size" value="29"/>
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199 <param name="correct_mer_threshold" value="19"/>
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200 <param name="correct_min_read_length" value="4001"/>
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201 <param name="correct_min_overlap_length" value="2001"/>
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202 <param name="correct_hash_bits" value="24"/>
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203 <param name="seed_min_length" value="29"/>
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204 <param name="seed_max_length" value="9999"/>
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205 <param name="align_bandwidth" value="14"/>
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206 <param name="score_fraction" value=".98"/>
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207 <param name="min_identity" value=".84"/>
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208 <param name="min_score" value="5001"/>
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209 <param name="end_clipping" value="99"/>
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210 <param name="incompatible_cutoff" value=".14"/>
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211 </section>
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212 <assert_command>
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213 <has_text_matching expression="verkko --hifi"/>
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214 <has_text_matching expression="--nano"/>
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215 <has_text_matching expression="--base-k 1003"/>
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216 <has_text_matching expression="--max-k 15001"/>
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217 <has_text_matching expression="--window 99"/>
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218 <has_text_matching expression="--split-bases 3000000001"/>
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219 <has_text_matching expression="--split-reads 150001"/>
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220 <has_text_matching expression="--min-ont-length 2"/>
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221 <has_text_matching expression="--correct-k-mer-size 29"/>
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222 <has_text_matching expression="--correct-mer-threshold 19"/>
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223 <has_text_matching expression="--correct-min-read-length 4001"/>
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224 <has_text_matching expression="--correct-min-overlap-length 2001"/>
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225 <has_text_matching expression="--correct-hash-bits 24"/>
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226 <has_text_matching expression="--seed-min-length 29"/>
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227 <has_text_matching expression="--seed-max-length 9999"/>
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228 <has_text_matching expression="--align-bandwidth 14 "/>
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229 <has_text_matching expression="--score-fraction 0.98"/>
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230 <has_text_matching expression="--min-identity 0.84"/>
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231 <has_text_matching expression="--min-score 5001"/>
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232 <has_text_matching expression="--end-clipping 99"/>
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233 <has_text_matching expression=" --incompatible-cutoff 0.14"/>
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234 </assert_command>
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235 <assert_stderr>
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236 <has_text text="job count min threads max threads"/>
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237 </assert_stderr>
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238 </test>
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239 <test expect_exit_code="1" expect_failure="true">
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240 <!-- No nano, use haplo, no canu correction -->
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241 <param name="hifi" value="test5.fastq,test1.fastq.gz"/>
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242 <section name="algorithm">
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243 <conditional name="hap_kmer">
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244 <param name="hap_kmers" value="yes"/>
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245 <param name="h1" value="1.meryldb"/>
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246 <param name="h2" value="2.meryldb"/>
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247 <param name="type" value="trio"/>
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248 </conditional>
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249 <param name="no-correction" value=""/>
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250 </section>
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251 <assert_command>
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252 <has_text_matching expression="verkko --hifi"/>
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253 <has_text_matching expression="--no-nano"/>
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254 <has_text_matching expression="--hap-kmers 'h1.meryl' 'h2.meryl' trio"/>
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255 </assert_command>
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256 <assert_stderr>
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257 <has_text text="job count min threads max threads"/>
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258 </assert_stderr>
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259 </test>
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260 </tests>
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261 <help><![CDATA[
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262 Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads. Verkko is Finnish for net, mesh and graph.
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263
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264 Verkko uses Canu to correct remaining errors in the HiFi reads, builds a multiplex de Bruijn graph using MBG, aligns the Oxford Nanopore reads to the graph using GraphAligner, progressively resolves loops and tangles first with the HiFi reads then with the aligned Oxford Nanopore reads, and finally creates contig consensus sequences using Canu's consensus module.
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265 ]]></help>
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266 <citations>
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267 <citation type="doi">10.1101/2022.06.24.497523</citation>
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268 </citations>
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269 </tool>