Mercurial > repos > iuc > trycycler_reconcile_msa

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e9abd8b86133e530d0395d85bca320a1af27a9b6
author iuc
date Tue, 02 Apr 2024 08:29:11 +0000
parents cb1e3db43020
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1 <tool id="trycycler_reconcile_msa" name="Trycycler reconcile/msa" version="@TOOL_VERSION@" profile="20.01">
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2 <description>reconcile the contigs within each cluster and perform a multiple sequence alignment</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam_ontology" />
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7 <expand macro="requirements" />
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8 <version_command>trycycler --version</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #import re
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11 #set $name = re.sub('[^\w\-\.]', '_', str($input_cluster.element_identifier)+".fasta")
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12 #set $folder = $name.strip(".fasta")
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13 #set $fullpath = "/".join(["selected_cluster",$folder])
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14 mkdir -p "${fullpath}/1_contigs" &&
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15 ln -s "${input_cluster}" "selected_cluster/${name}" &&
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16 python3 "$__tool_directory__"/trycycler.py reconcile "selected_cluster/${name}" &&
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17 trycycler reconcile --cluster_dir "${fullpath}"
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18 --reads $reads
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19 #if $linear
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20 --linear
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21 #end if
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22 --max_mash_dist $initial_ckeck.max_mash_dist
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23 --max_length_diff $initial_ckeck.max_length_diff
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24 --max_add_seq $circularisation.max_add_seq
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25 --max_add_seq_percent $circularisation.max_add_seq_percent
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26 --max_trim_seq $circularisation.max_trim_seq
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27 --max_trim_seq_percent $circularisation.max_trim_seq_percent
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28 --min_identity $final_check.min_identity
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29 --min_1kbp_identity $final_check.min_1kbp_identity
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30 --threads \${GALAXY_SLOTS:-2} &&
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31 trycycler msa --cluster_dir "$fullpath"
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32 --kmer $msa.kmer
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33 --step $msa.step
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34 --lookahead $msa.lookahead
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35 --threads \${GALAXY_SLOTS:-2} &&
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36 mv '${fullpath}/2_all_seqs.fasta' '$reconciled_cluster' &&
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37 mv '${fullpath}/3_msa.fasta' '$aligned_cluster'
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38 ]]> </command>
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39 <inputs>
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40 <param name="input_cluster" type="data" format="fasta" label="Cluster multi-FASTA dataset" help="The input should be an independent cluster generated by the *trycycler cluster* tool" />
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41 <param name="reads" type="data" format="fastq,fastq.gz" label="Long-read datasets" help="Long reads (FASTQ format) used to generate the assemblies" />
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42 <param argument="--linear" type="boolean" truevalue="--linear" falsevalue="" label="Input contigs are not circular" help="Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile." />
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43 <section name='initial_ckeck' title='Reconcile initial check options' expanded='true'>
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44 <param argument="--max_mash_dist" type="float" min="0" max="0.2" value="0.02" label="Max Mash distance" help="If any of the sequences have a pairwise Mash distance of more than this (default = 0.02), then the contigs will fail the initial check." />
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45 <param argument="--max_length_diff" type="float" min="1" max="2" value="1.1" label="Max relative length factor" help="If any of the sequences have a pairwise relative length factor of more than this, then the contigs will fail the initial check. For example, if set to 1.1 (the default), then no contig can be more than 10% longer than any other." />
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46 </section>
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47 <section name="circularisation" title="Reconcile circularization options" expanded='true'>
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48 <param argument="--max_add_seq" type="integer" min="0" max="4000" value="1000" label="Max number of pb to add to circularize" help="If they are set to 1000, then Trycycler will be willing to add up to 1000 bp to circularise it. Any contig which requires more than 1000 bp added to circularise will cause Trycycler reconcile to fail." />
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49 <param argument="--max_add_seq_percent" type="integer" min="0" max="10" value="5" label="Max percentage of a contig length to add to circularize" help="If they are set to 5, then Trycycler will be willing to add up to 5% of a contig's length to circularise it. Any contig which requires more than 5% of its length added to circularise will cause Trycycler reconcile to fail." />
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50 <param argument="--max_trim_seq" type="integer" min="0" max="100000" value="50000" label="Max number of pb to trim to circularize" help="If they are set to 50000, then Trycycler will be willing to remove up to 5000 bp to circularise it. Any contig which requires more than 5000 bp removed to circularise will cause Trycycler reconcile to fail." />
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51 <param argument="--max_trim_seq_percent" type="integer" min="0" max="20" value="10" label="Max percentage of a contig length to trim to circularize" help="If they are set to 10, then Trycycler will be willing to remove up to 10% of a contig's length to circularise it. Any contig which requires more than 10% of its length removed to circularise will cause Trycycler reconcile to fail." />
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52 </section>
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53 <section name="final_check" title="Reconcile final check" expanded="true">
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54 <param argument="--min_identity" type="integer" min="70" max="100" value="98" label="Min global alignment percentage identity" help="If any of the sequences have a pairwise global alignment percent identity of less than this (default = 98), then the contigs will fail the final check." />
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55 <param argument="--min_1kbp_identity" type="integer" min="0" value="25" label="Minimum allowed pairwise 1kbp window identity" help="If any of the sequences have lower pairwise window identity, it is discarted." />
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56 </section>
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57 <section name="msa" title="Multiple sequence alignment (MSA) options" expanded="true">
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58 <param argument="--kmer" type="integer" min="20" max="45" value="32" label="k-mer size" help="The k-mer size used for sequence partitioning (default = 32)" />
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59 <param argument="--step" type="integer" min="500" max="1500" value="1000" label="Step size" help="The step size used for sequence partitioning (default = 1000)." />
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60 <param argument="--lookahead" type="integer" min="500" max="1500" value="1000" label="Look-ahead margin" help="The look-ahead margin used for sequence partitioning (default = 10000)." />
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61 </section>
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62
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63 </inputs>
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64 <outputs>
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65 <data name="reconciled_cluster" format="fasta" label="Trycycler reconcile on ${input_cluster.element_identifier}" from_work_dir="selected_cluster" />
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66 <data name="aligned_cluster" format="fasta" label="Trycycler msa on ${input_cluster.element_identifier}" from_work_dir="selected_clusters" />
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67 </outputs>
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68 <tests>
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69 <test>
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70 <param name='input_cluster' value='cluster_01.fasta' />
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71 <param name="reads" value="reads.fastq.gz" />
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72 <output name='reconciled_cluster' file='reconciled_cluster_01.fasta' />
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73 <output name='aligned_cluster' file='aligned_cluster_01.fasta' />
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74 </test>
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75 <test>
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
76 <param name='input_cluster' value='cluster_01.fasta' />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
77 <param name="reads" value="reads.fastq.gz" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
78 <section name="initial_check">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
79 <param name="max_mash_dist" value="0.3" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
80 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
81 <section name="circularisation">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
82 <param name="max_add_seq_percent" value="7" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
83 <param name="max_trim_seq" value="47000" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
84 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
85 <section name="final_check">
5
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
86 <param name="min_1kbp_identity" value="30" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
87 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
88 <section name="msa">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
89 <param name="kmer" value="30" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
90 </section>
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
91 <output name='reconciled_cluster' file='reconciled_cluster_02.fasta' />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
92 <output name='aligned_cluster' file='aligned_cluster_02.fasta' />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
93 </test>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
94 <test>
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
95 <param name='input_cluster' value='cluster_01.fasta' />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
96 <param name="reads" value="reads.fastq.gz" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
97 <section name="initial_check">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
98 <param name="max_mash_dist" value="0.3" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
99 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
100 <section name="circularisation">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
101 <param name="max_add_seq" value="900" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
102 <param name="max_trim_seq" value="45000" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
103 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
104 <section name="final_check">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
105 <param name="min_identity" value="97" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
106 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
107 <section name="msa">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
108 <param name="step" value="1100" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
109 </section>
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
110 <output name='reconciled_cluster' file='reconciled_cluster_03.fasta' />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
111 <output name='aligned_cluster' file='aligned_cluster_03.fasta' />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
112 </test>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
113 <test>
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
114 <param name='input_cluster' value='cluster_01.fasta' />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
115 <param name="reads" value="reads.fastq.gz" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
116 <section name="initial_check">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
117 <param name="max_length_diff" value="1.2" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
118 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
119 <section name="circularisation">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
120 <param name="max_add_seq" value="920" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
121 <param name="max_trim_seq_percent" value="12" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
122 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
123 <section name="final_check">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
124 <param name="min_identity" value="95" />
5
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
125 <param name="min_1kbp_identity" value="25" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
126 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
127 <section name="msa">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
128 <param name="kmer" value="33" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
129 </section>
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
130 <output name='reconciled_cluster' file='reconciled_cluster_04.fasta' />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
131 <output name='aligned_cluster' file='aligned_cluster_04.fasta' />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
132 </test>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
133 <test>
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
134 <param name='input_cluster' value='cluster_01.fasta' />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
135 <param name="reads" value="reads.fastq.gz" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
136 <section name="initial_check">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
137 <param name="max_mash_dist" value="0.3" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
138 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
139 <section name="circularisation">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
140 <param name="max_add_seq_percentage" value="8" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
141 <param name="max_trim_seq" value="45300" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
142 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
143 <section name="final_check">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
144 <param name="min_identity" value="97" />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
145 </section>
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
146 <section name="msa">
1
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
147 <param name="step" value="1100" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
148 <param name="lookahead" value="980" />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
149 </section>
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
150 <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' />
b64696992ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
iuc
parents: 0
diff changeset
151 <output name='aligned_cluster' file='aligned_cluster_05.fasta' />
0
4ac81df20c74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
152 </test>
5
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
153 <test>
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
154 <!-- Use similar collection elmement file id as input (wihout extension)-->
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
155 <param name='input_cluster' value='cluster_01' />
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
156 <param name="reads" value="reads.fastq.gz" />
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
157 <section name="initial_check">
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
158 <param name="max_mash_dist" value="0.3" />
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
159 </section>
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
diff changeset
160 <section name="circularisation">
cb1e3db43020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
iuc
parents: 3
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161 <param name="max_add_seq_percentage" value="8" />
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162 <param name="max_trim_seq" value="45300" />
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163 </section>
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164 <section name="final_check">
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165 <param name="min_identity" value="97" />
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166 </section>
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167 <section name="msa">
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168 <param name="step" value="1100" />
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169 <param name="lookahead" value="980" />
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170 </section>
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171 <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' />
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172 <output name='aligned_cluster' file='aligned_cluster_05.fasta' />
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173 </test>
0
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174 </tests>
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175 <help><![CDATA[
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176
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177 .. class:: infomark
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178
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179 **Purpose**
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180
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181 This tool integrates two Trycycle commands: **Trycycler reconcile** and **Trycycler msa**.
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182
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183 The **Trycycler reconcile** tool carries out four routines:
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184
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185 ::
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186
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187 * Perform an initial check to make sure the contigs look sufficiently similar to each other.
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188 * Ensure that all contig sequences are on the same strand.
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189 * If the replicon is circular it fixes any circularisation issues (i.e. add/remove sequence at each contig's start/end as necessary)
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190 * Perform a final alignment check to make sure the normalised/circularised contigs are sufficiently similar to each other for the next step
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191
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192 After that, **Trycycler msa** takes the reconciled contig sequences and runs a multiple sequence alignment.
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193
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194 ----
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195
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196 .. class:: infomark
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197
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198 **Input**
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199
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200 This tool requires the clustered contings generated by the **Trycycle cluster** tool, as well as the long-read dataset with **Trycycler cluster**.
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201
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202
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203 ----
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204
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205 .. class:: infomark
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206
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207 **Output**
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208
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209 **Trycycler reconcile/msa** generates two datasets:
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210
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211 ::
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212
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213 * A multi-FASTA file dataset for each contig ready for multiple sequence alignment.
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214 * A FASTA-formatted multiple sequence alignment for each contig ready for use in generating a consensus.
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215
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216 ----
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217
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218 .. class:: infomark
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219
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220 **Manual intervention**
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221
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222 Trycycler reconcile may not complete successfully, in which case you will have to intervene and run it again. Often this simply means excluding whichever contig is causing the problem, usually due to significant length differences between contigs, or particularly bad pairwise identity or large insertion/deletion. It can be done by using the **Filter sequences by length** tool.
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223
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224 Throwing out troublesome contigs at this step is normal. To prepare a set of reduduntant assemblies aims to prevent that losing one or two would not be a problem.
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225
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226 You should aim to have around four to eight contigs left after running Trycycler reconcile. Less than that (two or three) will not provide as many variants for the next steps and may affect your consensus sequence quality. More than that (nine or more) is fine but probably won't be of any extra benefit. If you have too few contigs for your cluster, you might want to consider going back to the start of the pipeline and generating more input assemblies. If you have plenty of contigs, you can delete some of the worst ones and run Trycycler reconcile again. Use the final check to guide you: delete the contigs with the lowest identities and largest indels relative to the other contigs.
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227
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228 Unlike in previous steps of **Trycycler**, the msa step should be hands-off. I.e. no manual intervention is required – just run it and wait for it to finish.
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229
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230
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231 ----
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232
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233 .. class:: infomark
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234
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235 @PIPELINE@
1
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236 ]]> </help>
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237 <expand macro='citations' />
0
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238 </tool>