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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
author iuc
date Mon, 15 Nov 2021 16:48:46 +0000
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d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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1 <tool id="hypo" name="HyPo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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2 <description>super fast and accurate polisher for long read genome assemblies</description>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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3 <macros>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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4 <import>macros.xml</import>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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5 </macros>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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6 <expand macro='requirements' />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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7 <expand macro='xrefs'/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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9 #for $i, $fastq in enumerate($reads_short):
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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10 #if $fastq.ext.endswith(".gz")
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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11 #set $ext='.fastq.gz'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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12 #else
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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13 #set $ext='.fastq'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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14 #end if
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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15 ln -s '$fastq' 'read_$i$ext' &&
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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16 echo 'read_$i$ext' >> short_reads.txt &&
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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17 #end for
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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18 hypo
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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19 --reads-short @short_reads.txt
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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20 --draft '$draft'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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21 --bam-sr '$bam_sr'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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22 #if $bam_lr
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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23 --bam-lr '$bam_lr'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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24 #end if
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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25 --coverage-short $coverage_short
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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26 --size-ref '$size_ref'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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27 --kind-sr $kind_sr
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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28
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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29 #if $advanced_options.processing_size
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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30 --processing-size $advanced_options.processing_size
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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31 #end if
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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32 --match-sr $advanced_options.match_sr
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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33 --mismatch-sr $advanced_options.mismatch_sr
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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34 --gap-sr $advanced_options.gap_sr
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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35 --match-lr $advanced_options.match_lr
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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36 --mismatch-lr $advanced_options.mismatch_lr
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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37 --gap-lr $advanced_options.gap_lr
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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38 --ned-th $advanced_options.ned_th
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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39 --qual-map-th $advanced_options.qual_map_th
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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40 -o '$out_fasta'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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41 -t \${GALAXY_SLOTS:-4}
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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42 #if $advanced_options.log == 'true'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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43 > '$out_log'
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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44 #end if
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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45 ]]></command>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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46 <inputs>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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47 <param argument="--reads-short" type="data" format="fastq,fastq.gz" multiple="true" label="Illumina FASTQ files" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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48 <param argument="--draft" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Draft genome assembly"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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49 <param argument="--bam-sr" type="data" format="bam" label="BAM with illumina read alignments"
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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50 help="Input file name containing the alignments of short reads against the draft (must have CIGAR information)"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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51 <param argument="--bam-lr" type="data" format="bam" optional="true" label="BAM with ONT reads aligned"
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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52 help="Input file name containing the alignments of long reads against the draft (must have CIGAR information).
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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53 Optional (only Short reads polishing will be performed if this argument is not given)"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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54 <param argument="--coverage-short" type="integer" value="" min="0" label="Aproximate mean coverage of the short reads"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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55 <param argument="--size-ref" type="text" label="Aproximate size of the genome" help="A number can be followed by units k/m/g; e.g. 10m, 2.3g.">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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56 <sanitizer invalid_char="">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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57 <valid initial="string.letters,string.digits">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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58 <add value="." />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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59 </valid>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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60 </sanitizer>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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61 <validator type="regex">[A-Za-z0-9\.]+</validator>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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62 </param>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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63 <param argument="--kind-sr" type="select" label="Type of short reads">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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64 <option value="sr" selected="true">Corresponding to NGS reads like Illumina reads (sr)</option>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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65 <option value="ccs">Corresponding to HiFi reads like PacBio CCS reads (ccs)</option>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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66 </param>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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67 <section name="advanced_options" title="Advanced options">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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68 <param argument="--match-sr" type="integer" value="5" label="Score for matching bases for short reads" help="Default value is 5"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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69 <param argument="--mismatch-sr" type="integer" value="-4" label="Score for mismatching bases for short reads" help="Default value is -4"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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70 <param argument="--gap-sr" type="integer" value="-8" max="0" label="Gap penalty for short reads" help="Default value is -8 (must be negative)"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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71 <param argument="--match-lr" type="integer" min="0" value="3" label="Score for matching bases for long reads" help="Default value is 3"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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72 <param argument="--mismatch-lr" type="integer" value="-5" label="Score for mismatching bases for long reads" help="Default value is -5"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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73 <param argument="--gap-lr" type="integer" value="-4" max="0" label="Gap penalty for long reads" help="Default value is -4 (must be negative)"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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74 <param argument="--ned-th" type="integer" value="20" label="Threshold for NED"
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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75 help="Threshold for Normalised Edit Distance of long arms allowed in a window (in percentage). Higher number means more arms allowed which
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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76 may slow down the execution. Default value is 20" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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77 <param argument="--qual-map-th" type="integer" value="2" label="Threshold for mapping quality of reads"
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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78 help="The reads with mapping quality below this threshold will not be taken into consideration. Default value is 2" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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79 <param argument="--processing-size" type="integer" optional="true" label="Number of contigs to be processed in one batch" help="Lower value means less memory usage but slower speed. By default, all the contigs in the draft"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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80 <param name="log" type="boolean" truevalue="true" falsevalue="false" label="Generate log file"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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81 </section>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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82 </inputs>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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83 <outputs>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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84 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string}: polished assembly"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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85 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log file">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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parents:
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86 <filter>advanced_options['log']</filter>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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87 </data>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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88 </outputs>
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89 <tests>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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90 <!--Test 01-->
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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91 <test expect_num_outputs="1">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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92 <param name="draft" value="draft_genome.fasta" ftype="fasta"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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93 <param name="reads_short" value="Illumina_01.fastq.gz,Illumina_02.fastq.gz" ftype="fastq.gz"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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94 <param name="size_ref" value="10k" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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95 <param name="coverage_short" value="35"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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96 <param name="bam_sr" value="short_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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97 <output name="out_fasta" file="test_01.fasta" ftype="fasta" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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98 </test>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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99 <!--Test 02: test long-reads BAM-->
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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100 <test expect_num_outputs="1">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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101 <param name="draft" value="draft_genome.fasta" ftype="fasta"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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102 <param name="reads_short" value="Illumina_01.fastq.gz,Illumina_02.fastq.gz" ftype="fastq.gz"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
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103 <param name="size_ref" value="10k" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
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104 <param name="coverage_short" value="35"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
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105 <param name="bam_sr" value="short_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
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106 <param name="bam_lr" value="long_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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107 <output name="out_fasta" file="test_02.fasta" ftype="fasta" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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108 </test>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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109 <!--Test 03: test css option in type of short reads-->
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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110 <test expect_num_outputs="1">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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111 <param name="draft" value="draft_genome.fasta" ftype="fasta"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
112 <param name="reads_short" value="Illumina_01.fastq.gz,Illumina_02.fastq.gz" ftype="fastq.gz"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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113 <param name="size_ref" value="10k" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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114 <param name="coverage_short" value="35"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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115 <param name="bam_sr" value="short_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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116 <param name="bam_lr" value="long_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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117 <param name="kind-sr" value="css"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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118 <output name="out_fasta" file="test_03.fasta" ftype="fasta" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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119 </test>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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120 <!--Test 04: test processing-size parameter -->
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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121 <test expect_num_outputs="1">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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122 <param name="draft" value="draft_genome.fasta" ftype="fasta"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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diff changeset
123 <param name="reads_short" value="Illumina_01.fastq.gz,Illumina_02.fastq.gz" ftype="fastq.gz"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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124 <param name="size_ref" value="10k" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
125 <param name="coverage_short" value="35"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
126 <param name="bam_sr" value="short_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
127 <param name="bam_lr" value="long_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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128 <section name="advanced_options">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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129 <param name="processing-size" value="2"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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130 </section>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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diff changeset
131 <output name="out_fasta" file="test_04.fasta" ftype="fasta" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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132 </test>
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133 <!--Test 05: test log option-->
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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134 <test expect_num_outputs="2">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
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diff changeset
135 <param name="draft" value="draft_genome.fasta" ftype="fasta"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
136 <param name="reads_short" value="Illumina_01.fastq.gz,Illumina_02.fastq.gz" ftype="fastq.gz"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
137 <param name="size_ref" value="10k" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
138 <param name="coverage_short" value="35"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
139 <param name="bam_sr" value="short_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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parents:
diff changeset
140 <param name="log" value="true"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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parents:
diff changeset
141 <output name="out_fasta" file="test_05.fasta" ftype="fasta" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
142 <output name="out_log" ftype="txt">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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parents:
diff changeset
143 <assert_contents>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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parents:
diff changeset
144 <has_text text="No. of k-mers below min. threshold"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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parents:
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145 <has_text text="Info: Value of K chosen for the given genome size"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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parents:
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146 </assert_contents>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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147 </output>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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148 </test>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
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parents:
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149 <!--Test 06: advanced all options-->
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
150 <test expect_num_outputs="1">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
151 <param name="draft" value="draft_genome.fasta" ftype="fasta"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
152 <param name="reads_short" value="Illumina_01.fastq.gz,Illumina_02.fastq.gz" ftype="fastq.gz"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
153 <param name="size_ref" value="10k" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
154 <param name="coverage_short" value="35"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
155 <param name="bam_sr" value="short_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
156 <param name="bam_lr" value="long_reads.bam" ftype="bam" />
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
157 <section name="advanced_options">
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
158 <param name="match_sr" value="4"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
159 <param name="mismatch_sr" value="-2"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
160 <param name="gap_sr" value="-10"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
161 <param name="match_lr" value="3"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
162 <param name="mismatch_lr" value="-7"/>
d7c48cf1bf50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo commit 2151cc2f0b32a242d8a18537f0bdfb92b907548a"
iuc
parents:
diff changeset
163 <param name="gap_lr" value="-15"/>
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164 <param name="ned_th" value="10"/>
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165 <param name="qual_map_th" value="4"/>
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166 </section>
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167 <output name="out_fasta" file="test_06.fasta" ftype="fasta" />
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168 </test>
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169 <!--Test 07: test fastq files-->
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170 <test expect_num_outputs="1">
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171 <param name="draft" value="draft_genome.fasta" ftype="fasta"/>
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172 <param name="reads_short" value="Illumina_01.fastq,Illumina_02.fastq" ftype="fastq"/>
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173 <param name="size_ref" value="10k" />
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174 <param name="coverage_short" value="35"/>
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175 <param name="bam_sr" value="short_reads.bam" ftype="bam" />
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176 <output name="out_fasta" file="test_07.fasta" ftype="fasta" />
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177 </test>
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178 </tests>
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179 <help><![CDATA[
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180
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181 .. class:: infomark
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182
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183 **Purpose**
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184
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185 HyPo - a Hybrid Polisher - utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.
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186 It exploits unique genomic kmers to selectively polish segments of contigs using partial order alignment of selective read-segments.
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187 As demonstrated on human genome assemblies, Hypo generates significantly more accurate polished assembly in about one-third time with
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188 about half the memory requirements in comparison to contemporary widely used polishers like Racon.
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189
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190 Please note that "short reads" doesn't necessarily have to be NGS short reads; HiFi genomic reads (e.g. CCS) like those generated from PacBio SequelII
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191 could also be used instead. The requirement is that those reads should be highly accurate (>98% accuracy).
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192
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193 -------------------
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194
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195 .. class:: infomark
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196
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197 **Input files**
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198
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199 Hypo requires the following as input:
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200 * Short reads/HiFi reads (in FASTA/FASTQ format; can be compressed)
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201 * Draft contigs (in FASTA/FASTQ format; can be compressed)
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202 * Alignments between short reads (or HiFi reads) and the draft (hould contain CIGAR). If long reads are also to be used for polishing, then alignments between long reads and the draft.
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203 * Expected mean coverage of short reads (or HiFi reads) and approximate size of the genome.
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204
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205 In what follows, short reads can be replaced with HiFi reads.
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206
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207 -------------------
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208
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209 .. class:: infomark
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210
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211 **How it works**
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212
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213 Broadly, we (conceptually) divide a draft (uncorrected) contig into two types of regions (segments): strong and weak.
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214
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215 Strong regions are those which have strong evidence (support) of their correctness and
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216 thus do not need polishing. Weak regions, on the other hand, will be polished using POA. Each weak region will
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217 be polished using either short reads or long reads; short reads taking precedence over long reads. To identify
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218 strong regions, we make use of solid kmers (expected unique genomic kmers). Strong regions also play a role in
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219 selecting the read-segments to polish their neighbouring weak regions. Furthermore, our approach takes into account
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220 that the long reads and thus the assemblies generated from them are prone to homopolymer errors as mentioned in the beginning.
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221
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222 ]]></help>
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223 <expand macro="citations" />
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224 </tool>