Mercurial > repos > iuc > trycycler_cluster

annotate trycycler_cluster.xml @ 0:c767a45616d0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
author iuc
date Thu, 11 Feb 2021 19:26:49 +0000
parents
children 189e837009c9
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c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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1 <tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='21.01'>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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2 <description>cluster the contigs of your input assemblies into per-replicon groups</description>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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3 <macros>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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4 <import>macros.xml</import>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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5 </macros>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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6 <expand macro='edam_ontology'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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7 <expand macro='requirements'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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8 <version_command>trycycler --version</version_command>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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9 <command detect_errors='exit_code'><![CDATA[
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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10 #import re
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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11 mkdir -p initial_clusters assemblies &&
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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12 #for $input_file in $assemblies
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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13 #set $name = re.sub('[^\w\-\.]', '_', str($input_file.element_identifier))
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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14 ln -s '$input_file' 'assemblies/$name' &&
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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15 #end for
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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16 trycycler cluster --assemblies assemblies/*
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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17 --reads '$reads'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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18 --min_contig_len $min_contig_len
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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19 --min_contig_depth $min_contig_depth
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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20 --distance $distance
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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21 --threads \${GALAXY_SLOTS:-2}
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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22 --out_dir 'initial_clusters' &&
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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23 mv initial_clusters/contigs.phylip '$output_phylip' &&
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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24 mv initial_clusters/contigs.newick '$output_newick' &&
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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25 python3 '$__tool_directory__/trycycler.py' 'cluster' 'initial_clusters'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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26 ]]></command>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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27 <inputs>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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28 <param name='assemblies' type='data'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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29 format='fasta,fasta.gz' multiple='true' label='Assembled sequences datasets'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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30 help='Input assemblies whose contigs will be clustered (multiple FASTA files)' />
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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31 <param name='reads' type='data'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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32 format='fastq,fastq.gz' label='Long-read datasets'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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33 help='Long reads (FASTQ format) used to generate the assemblies' />
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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34 <param argument='--min_contig_len' type='integer'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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35 min='100' max='5000' value='1000' label='Minimun contig length'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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36 help='Contigs shorter than this are thrown out on the assumption that they are either incomplete or spurious. The default value is 1000, as plasmids smaller than that are very rare.' />
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
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37 <param argument='--min_contig_depth' type='float'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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38 min='0.01' max='1' value='0.1' label='Minimun contig depth'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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39 help='This controls how Trycycler filters out contigs with a low read depth. It is a multiple of the mean read depth for the assembly. For example, if an assembly has a mean depth of 90x and this setting is 0.1 (the default), then any contig with depth lower that x9 will be removed.'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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40 <param argument='--distance' type='float'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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41 min='0.001' max='0.1' value='0.01' label='Mash distance threshold'
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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42 help='This is the Mash distance threshold used when defining clusters, and the default threshold is 0.01. Smaller thresholds (e.g. 0.005) can result in a larger number of tighter clusters. Larger thresholds (e.g. 0.02) can result in a smaller number of looser clusters.' />
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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43 </inputs>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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44 <outputs>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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45 <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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46 <data name='output_newick' format='newick' label='${tool.name} on ${on_string}: newick'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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47 <collection name='initial_clusters' type='list' label='${tool.name} on ${on_string}'>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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48 <discover_datasets pattern='__designation_and_ext__' format='fasta' directory='initial_clusters'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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49 </collection>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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50 </outputs>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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51 <tests>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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52 <test>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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53 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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54 <param name='reads' value='reads.fastq.gz'/>
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55 <output name='output_phylip' file='contigs_01.phylip'/>
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56 <output name='output_newick' file='contigs_01.newick'/>
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57 <output_collection name='initial_clusters' type='list' count='2'>
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58 <element name='cluster_01' file='cluster_01.fasta' ftype='fasta' lines_diff='20'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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59 </output_collection>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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60 </test>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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61 <test>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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62 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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63 <param name='reads' value='reads.fastq.gz'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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64 <param name='min_contig_len' value='900'/>
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65 <param name='min_contig_depth' value='0.05'/>
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66 <param name='distance' value='0.05'/>
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67 <output name='output_phylip' file='contigs_02.phylip'/>
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68 <output name='output_newick' file='contigs_02.newick'/>
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69 <output_collection name='initial_clusters' type='list' count='2'>
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70 <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20'/>
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71 </output_collection>
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72 </test>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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73 <test>
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74 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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75 <param name='reads' value='reads.fastq.gz'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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76 <param name='min_contig_len' value='850'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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77 <param name='min_contig_depth' value='0.01'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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78 <param name='distance' value='0.09'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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79 <output name='output_phylip' file='contigs_03.phylip'/>
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80 <output name='output_newick' file='contigs_03.newick'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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81 <output_collection name='initial_clusters' type='list' count='2'>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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82 <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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83 </output_collection>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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84 </test>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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85 <test>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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86 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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87 <param name='reads' value='reads.fastq.gz'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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88 <param name='min_contig_len' value='1100'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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89 <param name='min_contig_depth' value='0.02'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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90 <param name='distance' value='0.07'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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91 <output name='output_phylip' file='contigs_04.phylip'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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92 <output name='output_newick' file='contigs_04.newick'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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93 <output_collection name='initial_clusters' type='list' count='2'>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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94 <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20'/>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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95 </output_collection>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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96 </test>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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97 </tests>
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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98 <help><![CDATA[
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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99 .. class:: infomark
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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100
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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101 **Purpose**
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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102
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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103 The *Trycycler cluster* tool carries out complete-linkage clustering of all contig sequences based on their `Mash distance <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x/>`_, a fast sequence distance estimator that uses the MinHash algorithm. It also serves to exclude any spurious, incomplete or badly misassembled contigs.
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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104
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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105 If your contigs do not form clear clusters, that indicates that the input assemblies are inconsistent and unreliable. If you find yourself in this situation (struggling to identify which clusters are good and which are bad), then you probably need to get better long-read data (longer and/or deeper) and try again.
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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106
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107 ----
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108
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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109 .. class:: infomark
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110
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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111 **Input**
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112
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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113 This tool requires two different inputs: a set of multiple separate assemblies and a long-read set.
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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114
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115 ----
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116
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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117 .. class:: infomark
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118
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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119 **Output**
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120
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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121 **Trycycler cluster** generates three files:
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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122
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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123 \* A matrix of the Mash distances between contigs (phylip output).
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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124
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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125 \* A `FastMe tree <https://academic.oup.com/mbe/article/32/10/2798/1212138>`_ of the contigs built from the distance matrix. It can be visualised in the **newick display** tool.
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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126
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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127 \* A collection list which contains the clusters.
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128
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129 \
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130
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131 **Choose your clusters**
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132
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133 After running **Trycycler cluster**, you need to extract the cluster datasets from the collection by using the **Extract Element from a collection based on a name** tool. It is up to you to choose which of the clusters are good and which are bad. This can be somewhat subjective, so there is not an exact procedure for you to follow.
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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134
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135 Generally speaking, a good cluster contains many contigs (ideally one from each assembly) which are all very close to each other and have realistic read depths. A bad cluster contains a small number of contigs (maybe just one) which might have low read depths. The tree can be useful in making these decisions, though interpret it with a grain of salt, as the contig sequences are not necessarily related in a tree-like manner.
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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136
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137 If you have prior knowledge about what your genome should look like, that information can be quite useful in deciding which clusters are good. E.g. if you happened to know that your genome contains a 150 kbp plasmid, then you can expect one of your good clusters to have contigs of about that size.
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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138
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139 You might also decide at this point that the default value for --distance (0.01) was not quite right. E.g. if your tree contains two very close clusters that you think should actually be one cluster, you can run Trycycler cluster again with a larger distance threshold. Another thing to keep in mind: contamination can happen. I most often see this occur with cross-barcode contamination, where a contig in one assembly actually belongs to a different genome from the same multiplexed sequencing run.
c767a45616d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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140
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141
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142 ----
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143
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144 .. class:: infomark
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145
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146 @PIPELINE@
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147 ]]></help>
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148 <expand macro='citations'/>
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149 </tool>