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comparison trycycler_reconcile_msa.xml @ 5:cb1e3db43020 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db
author iuc
date Wed, 29 Mar 2023 20:24:48 +0000
parents b5e35a2ca4f3
children
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4:59bd28f6265d 5:cb1e3db43020
6 <expand macro="edam_ontology" /> 6 <expand macro="edam_ontology" />
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <version_command>trycycler --version</version_command> 8 <version_command>trycycler --version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #import re 10 #import re
11 #set $name = re.sub('[^\w\-\.]', '_', str($input_cluster.element_identifier)) 11 #set $name = re.sub('[^\w\-\.]', '_', str($input_cluster.element_identifier)+".fasta")
12 #set $folder = $name.strip(".fasta") 12 #set $folder = $name.strip(".fasta")
13 #set $fullpath = "/".join(["selected_cluster",$folder]) 13 #set $fullpath = "/".join(["selected_cluster",$folder])
14 mkdir -p "${fullpath}/1_contigs" && 14 mkdir -p "${fullpath}/1_contigs" &&
15 ln -s "${input_cluster}" "selected_cluster/${name}" && 15 ln -s "${input_cluster}" "selected_cluster/${name}" &&
16 python3 "$__tool_directory__"/trycycler.py reconcile "selected_cluster/${name}" && 16 python3 "$__tool_directory__"/trycycler.py reconcile "selected_cluster/${name}" &&
24 --max_add_seq $circularisation.max_add_seq 24 --max_add_seq $circularisation.max_add_seq
25 --max_add_seq_percent $circularisation.max_add_seq_percent 25 --max_add_seq_percent $circularisation.max_add_seq_percent
26 --max_trim_seq $circularisation.max_trim_seq 26 --max_trim_seq $circularisation.max_trim_seq
27 --max_trim_seq_percent $circularisation.max_trim_seq_percent 27 --max_trim_seq_percent $circularisation.max_trim_seq_percent
28 --min_identity $final_check.min_identity 28 --min_identity $final_check.min_identity
29 --max_indel_size $final_check.max_indel_size 29 --min_1kbp_identity $final_check.min_1kbp_identity
30 --threads \${GALAXY_SLOTS:-2} && 30 --threads \${GALAXY_SLOTS:-2} &&
31 trycycler msa --cluster_dir "$fullpath" 31 trycycler msa --cluster_dir "$fullpath"
32 --kmer $msa.kmer 32 --kmer $msa.kmer
33 --step $msa.step 33 --step $msa.step
34 --lookahead $msa.lookahead 34 --lookahead $msa.lookahead
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." /> 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." />
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." /> 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." />
52 </section> 52 </section>
53 <section name="final_check" title="Reconcile final check" expanded="true"> 53 <section name="final_check" title="Reconcile final check" expanded="true">
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." /> 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." />
55 <param argument="--max_indel_size" type="integer" min="0" max="10000" value="1000" label="Max alignment indel size" help="If any of the sequences have a pairwise alignment indel size of more than this (default = 1000), then the contigs will fail the final check." /> 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." />
56 </section> 56 </section>
57 <section name="msa" title="Multiple sequence alignment (MSA) options" expanded="true"> 57 <section name="msa" title="Multiple sequence alignment (MSA) options" expanded="true">
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)" /> 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)" />
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)." /> 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)." />
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)." /> 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)." />
81 <section name="circularisation"> 81 <section name="circularisation">
82 <param name="max_add_seq_percent" value="7" /> 82 <param name="max_add_seq_percent" value="7" />
83 <param name="max_trim_seq" value="47000" /> 83 <param name="max_trim_seq" value="47000" />
84 </section> 84 </section>
85 <section name="final_check"> 85 <section name="final_check">
86 <param name="max_indel_size" value="230" /> 86 <param name="min_1kbp_identity" value="30" />
87 </section> 87 </section>
88 <section name="msa"> 88 <section name="msa">
89 <param name="kmer" value="30" /> 89 <param name="kmer" value="30" />
90 </section> 90 </section>
91 <output name='reconciled_cluster' file='reconciled_cluster_02.fasta' /> 91 <output name='reconciled_cluster' file='reconciled_cluster_02.fasta' />
120 <param name="max_add_seq" value="920" /> 120 <param name="max_add_seq" value="920" />
121 <param name="max_trim_seq_percent" value="12" /> 121 <param name="max_trim_seq_percent" value="12" />
122 </section> 122 </section>
123 <section name="final_check"> 123 <section name="final_check">
124 <param name="min_identity" value="95" /> 124 <param name="min_identity" value="95" />
125 <param name="max_indel_size" value="230" /> 125 <param name="min_1kbp_identity" value="25" />
126 </section> 126 </section>
127 <section name="msa"> 127 <section name="msa">
128 <param name="kmer" value="33" /> 128 <param name="kmer" value="33" />
129 </section> 129 </section>
130 <output name='reconciled_cluster' file='reconciled_cluster_04.fasta' /> 130 <output name='reconciled_cluster' file='reconciled_cluster_04.fasta' />
148 <param name="lookahead" value="980" /> 148 <param name="lookahead" value="980" />
149 </section> 149 </section>
150 <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' /> 150 <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' />
151 <output name='aligned_cluster' file='aligned_cluster_05.fasta' /> 151 <output name='aligned_cluster' file='aligned_cluster_05.fasta' />
152 </test> 152 </test>
153 153 <test>
154 <!-- Use similar collection elmement file id as input (wihout extension)-->
155 <param name='input_cluster' value='cluster_01' />
156 <param name="reads" value="reads.fastq.gz" />
157 <section name="initial_check">
158 <param name="max_mash_dist" value="0.3" />
159 </section>
160 <section name="circularisation">
161 <param name="max_add_seq_percentage" value="8" />
162 <param name="max_trim_seq" value="45300" />
163 </section>
164 <section name="final_check">
165 <param name="min_identity" value="97" />
166 </section>
167 <section name="msa">
168 <param name="step" value="1100" />
169 <param name="lookahead" value="980" />
170 </section>
171 <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' />
172 <output name='aligned_cluster' file='aligned_cluster_05.fasta' />
173 </test>
154 </tests> 174 </tests>
155 <help><![CDATA[ 175 <help><![CDATA[
156 176
157 .. class:: infomark 177 .. class:: infomark
158 178