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comparison trycycler_consensus.xml @ 0:93c6a7423090 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 19:24:35 +0000
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children e59bee4565b3
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-1:000000000000 0:93c6a7423090
1 <tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='21.01'>
2 <description>generate a consensus contig sequence for each cluster</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro='edam_ontology'/>
7 <expand macro='requirements'/>
8 <version_command>trycycler --version</version_command>
9 <command detect_errors='exit_code'><![CDATA[
10 mkdir -p 'selected_cluster' &&
11 ln -s '${cluster_all_seqs}' 'selected_cluster/2_all_seqs.fasta' &&
12 ln -s '${reconcile_msa}' 'selected_cluster/3_msa.fasta' &&
13 ln -s '${partition_reads}' 'selected_cluster/4_reads.fastq' &&
14 trycycler consensus --cluster_dir 'selected_cluster'
15 #if $linear
16 --linear
17 #end if
18 --min_aligned_len $min_aligned_len
19 --min_read_cov $min_read_cov
20 --threads \${GALAXY_SLOTS:-2} &&
21 mv 'selected_cluster/7_final_consensus.fasta' $consensus
22 ]]></command>
23 <inputs>
24 <param name='cluster_all_seqs' type='data'
25 format='fasta' label='Reconciled cluster'
26 help='Reconciled sequences file' />
27 <param name='reconcile_msa' type='data'
28 format='fasta' label='Reconcile msa'
29 help='Multiple sequence alignment file' />
30 <param name='partition_reads' type='data'
31 format='fastq' label='Partition reads'
32 help='Partitioned reads' />
33 <param name='reads' type='data'
34 format='fastq,fastq.gz' label='Long-read datasets'
35 help='Long reads (FASTQ format) used to generate the assemblies' />
36 <param argument='--linear' type='boolean'
37 truevalue='--linear' falsevalue=''
38 label='Input contigs are not circular'
39 help='Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile.' />
40 <param argument='--min_aligned_len' type='integer' min='500' max='3500'
41 value='1000' label='Min bases aligned'
42 help='Reads with less than this many bases aligned (default = 1000) will be ignored.' />
43 <param argument='--min_read_cov' type='integer' min='0' max='100'
44 value='90' label='Min read length covered by alignments'
45 help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' />
46 </inputs>
47 <outputs>
48 <data name='consensus' format='fasta' label='${tool.name} on ${on_string}'/>
49 </outputs>
50 <tests>
51 <test>
52 <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta'/>
53 <param name='reconcile_msa' value='aligned_cluster_01.fasta'/>
54 <param name='partition_reads' value='partition_01.fastq'/>
55 <param name='reads' value='reads.fastq.gz'/>
56 <param name='min_aligned_len' value='1200'/>
57 <param name='min_read_cov' value='95'/>
58 <output name='consensus' file='consensus_sequence_01.fasta'/>
59 </test>
60 <test>
61 <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta'/>
62 <param name='reconcile_msa' value='aligned_cluster_02.fasta'/>
63 <param name='partition_reads' value='partition_01.fastq'/>
64 <param name='reads' value='reads.fastq.gz'/>
65 <param name='min_aligned_len' value='1100'/>
66 <param name='min_read_cov' value='90'/>
67 <output name='consensus' file='consensus_sequence_02.fasta'/>
68 </test>
69 <test>
70 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta'/>
71 <param name='reconcile_msa' value='aligned_cluster_03.fasta'/>
72 <param name='partition_reads' value='partition_01.fastq'/>
73 <param name='reads' value='reads.fastq.gz'/>
74 <param name='min_aligned_len' value='1300'/>
75 <param name='min_read_cov' value='97'/>
76 <output name='consensus' file='consensus_sequence_03.fasta'/>
77 </test>
78 <test>
79 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta'/>
80 <param name='reconcile_msa' value='aligned_cluster_03.fasta'/>
81 <param name='partition_reads' value='partition_01.fastq'/>
82 <param name='reads' value='reads.fastq.gz'/>
83 <param name='min_aligned_len' value='1000'/>
84 <param name='min_read_cov' value='87'/>
85 <output name='consensus' file='consensus_sequence_04.fasta'/>
86 </test>
87 </tests>
88 <help><![CDATA[
89
90 .. class:: infomark
91
92 **Purpose**
93
94 **Trycycler consensus** generate a consensus contig sequence for each cluster. It does this by converting the MSA into a graph form. When there is a tie between options, Trycycler aligns the reads to the alternative sequences and chooses the option with the best read alignment scores.
95
96 ::
97
98 GGAGGAGCTTTT-CGCCGCAGTCAACGAA-TAGCGTCTGAAAACGTGTATCAT
99 GGAGGAGCTTTTTCGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCAT
100 GGAGGAGCTTTTTCGCCGCAGTCAAC--ATTAGCGTCTGAAAACGTGTATCAT
101 GGAGGAGCTTTTTCGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCAT
102 GGAGGAGCTTTT-CGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCAT
103
104 From the hypothetical MSA, Trycycler generates a variation graph:
105
106 ::
107
108 ↗ - ↘ ↗ GAA- ↘
109 ↗ T ↘ ↗ --A- ↘
110 GGAGGAGCTTTT → T → CGCCGCAGTCAAC → --AT → TAGCGTCTGAAAACGTGTATCAT
111 ↘ T ↗ ↘ --A- ↗
112 ↘ - ↗ ↘ --A- ↗
113
114
115
116 The first thing Trycycler uses to choose variants is minimum total Hamming distance to the other variants. In cases of a minimum total Hamming distance tie, Trycycler will align the reads to each possibility and choose the option with the highest total read alignment score. Read alignment scores are calculated using a simple scheme: match score = 1, mismatch penalty = 1, gap open/extension penalty = 1. More information in the `documentation <https://github.com/rrwick/Trycycler/wiki/How-variants-are-chosen-for-the-consensus-sequence/>`_.
117
118
119
120 ----
121
122 .. class:: infomark
123
124 **Input**
125
126 This tool requires the output generated by **Trycylcler reconcile**, **Trycycler msa** and **Trycycler partition**.
127
128
129 ----
130
131 .. class:: infomark
132
133 **Output**
134
135 It generates a fasta file with the consesus sequence the cluster.
136
137
138 ----
139
140 .. class:: infomark
141
142 @PIPELINE@
143 ]]></help>
144 <expand macro='citations'/>
145 </tool>