annotate unicycler.xml @ 2:e92675014ac9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
author iuc
date Tue, 28 Nov 2017 10:53:47 -0500
parents f13d0498a199
children c4eac0c7e542
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.1">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
2 <macros>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
3 <token name="@VERSION@">0.4.1</token>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
4 </macros>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
5 <requirements>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
6 <requirement type="package" version="@VERSION@">unicycler</requirement>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
7 </requirements>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
9 ## Preparing files
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
10 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
12 #set fq1 = "fq1.fastq"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
13 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
14 #set fq1 = "fq1.fastq.gz"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
15 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
16 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
17 #set fq2 = "fq2.fastq"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
18 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
19 #set fq2 = "fq2.fastq.gz"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
20 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
21 ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
22 ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
23 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
24 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
25 #set fq1 = "fq1.fastq"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
26 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
27 #set fq1 = "fq1.fastq.gz"
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
28 #end if
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
29 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
30 #set fq2 = "fq2.fastq"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
31 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
32 #set fq2 = "fq2.fastq.gz"
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
33 #end if
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
34 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
35 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
36 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
37 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
38 #set fq = "fq.fastq"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
39 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
40 #set fq = "fq.fastq.gz"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
41 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
42 ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
43 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
44 #if $long
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
45 #if $long.is_of_type('fastqsanger')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
46 #set lr = "lr.fastq"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
47 #elif $long.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
48 #set lr = "lr.fastq.gz"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
49 #elif $long.is_of_type('fasta')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
50 #set lr = "lr.fasta"
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
51 #end if
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
52 ln -s '${long}' '$lr' &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
53 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
54 ## Get location for pilon installation
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
55 pilon=`pilon --jar_dir` &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
56 ## Running Unicycler
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
57 unicycler -t "\${GALAXY_SLOTS:-4}"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
58 -o ./
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
59 --verbosity 3
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
60 --pilon_path \$pilon
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
61 #if str( $paired_unpaired.fastq_input_selector ) != "single"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
62 -1 '$fq1'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
63 -2 '$fq2'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
64 #else
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
65 -s '$fq'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
66 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
67 #if $long
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
68 -l $lr
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
69 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
70 ## General Unicycler Options section
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
71 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
72 --mode '$mode'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
73 --min_fasta_length '$min_fasta_length'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
74 --linear_seqs '$linear_seqs'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
75 ## Spades Options section
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
76 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
77 $spades.no_correct
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
78 --min_kmer_frac '$spades.min_kmer_frac'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
79 --max_kmer_frac '$spades.max_kmer_frac'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
80 --kmer_count '$spades.kmer_count'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
81 --depth_filter '$spades.depth_filter'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
82 ## Rotation Options section
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
83 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
84 $rotation.no_rotate
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
85 #if $rotation.start_genes
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
86 --start_genes '$rotation.start_genes'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
87 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
88 --start_gene_id '$rotation.start_gene_id'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
89 --start_gene_cov '$rotation.start_gene_cov'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
90 ## Pilon Options section
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
91 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
92 $pilon.no_pilon
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
93 #if str($pilon.min_polish_size) != ''
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
94 --min_polish_size '$pilon.min_polish_size'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
95 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
96 ## Graph cleaning Options sdection
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
97 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
98 --min_component_size '$graph_clean.min_component_size'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
99 --min_dead_end_size '$graph_clean.min_dead_end_size'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
100 ## Long Read Alignment Options
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
101 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
102 #if $lr_align.contamination
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
103 --contamination '$lr_align.contamination'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
104 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
105 --scores '${lr_align.scores}'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
106 #if str($lr_align.low_score) != ''
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
107 --low_score '$lr_align.low_score'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
108 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
109 ## Miniasm requires racon, which is not available for python 3.x
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
110 --no_miniasm
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
111 ]]></command>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
112 <inputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
113 <conditional name="paired_unpaired">
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
114 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data">
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
115 <option selected="True" value="paired">Paired</option>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
116 <option value="paired_collection">Paired Collection</option>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
117 <option value="single">Single</option>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
118 </param>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
119 <when value="paired">
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
120 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
121 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
122 </when>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
123 <when value="paired_collection">
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
124 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
125 </when>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
126 <when value="single">
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
127 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
128 </when>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
129 </conditional>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
130 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
131 <param argument="--mode" type="select" label="Select Bridging mode">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
132 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
133 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
134 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
135 </param>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
136 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
137 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
138 <section name="spades" expanded="False" title="SPAdes options" help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!">
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
139 <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue="" label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
140 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
141 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
142 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
143 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
144 </section>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
145 <section name="rotation" expanded="false" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
146 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" label="Do not rotate completed replicons to start at a standard gene." help="Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence."/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
147 <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
148 <param argument="--start_gene_id" type="float" min="0" max="100" value="90" label="The minimum required BLAST percent identity for a start gene search"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
149 <param argument="--start_gene_cov" type="float" min="0" max="100" value="95" label="The minimum required BLAST percent coverage for a start gene search"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
150 </section>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
151 <section name="pilon" title="Pilon options" expanded="false">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
152 <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue="" label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
153 <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
154 </section>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
155 <section name="graph_clean" expanded="false" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete.">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
156 <param argument="--min_component_size" type="integer" min="0" value="1000" label="Unbridged graph components smaller than this size will be removed from the final graph" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
157 <param argument="--min_dead_end_size" type="integer" min="0" value="1000" label="Graph dead ends smaller than this size will be removed from the final graph"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
158 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
159 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
160 <param argument="--contamination" optional="true" type="data" format="fasta" label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
161 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
162 <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
163 </section>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
164 </inputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
165 <outputs>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
166 <data name="assembly_graph" format="txt" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
167 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
168 </outputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
169 <tests>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
170 <test>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
171 <conditional name="paired_unpaired">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
172 <param name="fastq_input_selector" value="paired" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
173 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
174 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
175 </conditional>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
176 <param name="mode" value="normal" />
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
177 <param name="min_fasta_length" value="100"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
178 <param name="linear_seqs" value="0"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
179 <section name="spades">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
180 <param name="no_correct" value="true"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
181 <param name="min_kmer_frac" value="0.2"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
182 <param name="max_kmer_frac" value="0.95"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
183 <param name="kmer_count" value="10"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
184 <param name="depth_filter" value="0.25"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
185 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
186 <section name="rotation">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
187 <param name="no_rotate" value=""/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
188 <param name="start_gene_id" value="90"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
189 <param name="start_gene_cov" value="95"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
190 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
191 <section name="pilon">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
192 <param name="no_pilon" value=""/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
193 <param name="min_polish_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
194 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
195 <section name="graph_clean">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
196 <param name="min_component_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
197 <param name="min_dead_end_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
198 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
199 <section name="lr_align">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
200 <param name="scores" value="3,-6,-5,-2"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
201 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
202 <output name="assembly_graph" ftype="txt">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
203 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
204 <has_text text="TACGGGGAAGGACGTC"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
205 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
206 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
207 <output name="assembly" ftype="fasta">
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
208 <assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
209 <has_text text="length=5386" />
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
210 </assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
211 </output>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
212 </test>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
213 <!--
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
214 Following test corresponds to the command:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
215
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
216 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
217 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
218 - -mode 'normal' - -no_correct
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
219
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
220 This command causes a segfault with the current version of unicycler on bioconda for Linux
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
221 during the minimap step (which seems to be compiled C code). A gist of the log can be found
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
222 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
223 -->
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
224 <test>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
225 <conditional name="paired_unpaired">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
226 <param name="fastq_input_selector" value="paired" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
227 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
228 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
229 </conditional>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
230 <param name="long" value="onp.fa" ftype="fasta" />
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
231 <param name="mode" value="normal" />
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
232 <param name="min_fasta_length" value="100"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
233 <param name="linear_seqs" value="0"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
234 <section name="spades">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
235 <param name="no_correct" value="true"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
236 <param name="min_kmer_frac" value="0.2"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
237 <param name="max_kmer_frac" value="0.95"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
238 <param name="kmer_count" value="10"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
239 <param name="depth_filter" value="0.25"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
240 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
241 <section name="rotation">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
242 <param name="no_rotate" value=""/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
243 <param name="start_gene_id" value="90"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
244 <param name="start_gene_cov" value="95"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
245 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
246 <section name="pilon">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
247 <param name="no_pilon" value=""/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
248 <param name="min_polish_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
249 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
250 <section name="graph_clean">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
251 <param name="min_component_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
252 <param name="min_dead_end_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
253 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
254 <section name="lr_align">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
255 <param name="scores" value="3,-6,-5,-2"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
256 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
257 <output name="assembly_graph" ftype="txt">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
258 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
259 <has_text text="TACGGGGAAGGACGTC" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
260 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
261 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
262 <output name="assembly" ftype="fasta">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
263 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
264 <has_text text="length=5386" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
265 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
266 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
267 </test>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
268 <test>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
269 <conditional name="paired_unpaired">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
270 <param name="fastq_input_selector" value="paired_collection"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
271 <param name="fastq_input1">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
272 <collection type="paired">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
273 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
274 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
275 </collection>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
276 </param>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
277 </conditional>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
278 <param name="mode" value="normal" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
279 <param name="min_fasta_length" value="100"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
280 <param name="linear_seqs" value="0"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
281 <section name="spades">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
282 <param name="no_correct" value="true"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
283 <param name="min_kmer_frac" value="0.2"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
284 <param name="max_kmer_frac" value="0.95"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
285 <param name="kmer_count" value="10"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
286 <param name="depth_filter" value="0.25"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
287 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
288 <section name="rotation">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
289 <param name="no_rotate" value=""/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
290 <param name="start_gene_id" value="90"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
291 <param name="start_gene_cov" value="95"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
292 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
293 <section name="pilon">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
294 <param name="no_pilon" value="true"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
295 <param name="min_polish_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
296 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
297 <section name="graph_clean">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
298 <param name="min_component_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
299 <param name="min_dead_end_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
300 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
301 <section name="lr_align">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
302 <param name="scores" value="3,-6,-5,-2"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
303 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
304 <output name="assembly_graph" ftype="txt">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
305 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
306 <has_text text="TACGGGGAAGGACGTC" />
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
307 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
308 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
309 <output name="assembly" ftype="fasta">
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
310 <assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
311 <has_text text="length=5386" />
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
312 </assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
313 </output>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
314 </test>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
315 </tests>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
316 <help><![CDATA[
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
317
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
318 **Unicycler**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
319
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
320 Unicycler is a hybrid assembly pipeline for bacterial genomes. It uses both Illumina reads and long reads (PacBio or Nanopore) to produce complete and accurate assemblies. It is written by `Ryan Wick`_ at the University of Melbourne's Centre for Systems Genomics. Much of the description below is lifted from Unicycler's `github page`_.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
321
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
322 .. _`Ryan Wick`: https://github.com/rrwick
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
323 .. _`github page`: https://github.com/rrwick/Unicycler
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
324
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
325 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
326
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
327 **Input data**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
328
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
329 Unicycler accepts inputs short (Illumina) reads in FASTQ format. Galaxy places additional requirement of having these in FASTQ format with `Sanger encoding`_ of quality scores. Long reads (from Oxford Nanopore or PacBio) can be either in FASTQ of FASTA form.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
330
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
331 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
332
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
333 The input options are::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
334
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
335 -1 SHORT1, --short1 SHORT1
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
336 FASTQ file of short reads (first reads in each pair)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
337 -2 SHORT2, --short2 SHORT2
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
338 FASTQ file of short reads (second reads in each pair)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
339 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
340 FASTQ file of unpaired short reads
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
341 -l LONG, --long LONG
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
342 FASTQ or FASTA file of long reads, if all reads are available at start.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
343
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
344 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
345
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
346 **Bridging mode**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
347
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
348 Unicycler can be run in three modes: conservative, normal (the default) and bold, set with the --mode option. Conservative mode is least likely to produce a complete assembly but has a very low risk of misassembly. Bold mode is most likely to produce a complete assembly but carries greater risk of misassembly. Normal mode is intermediate regarding both completeness and misassembly risk. See `description of modes`_ for more information.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
349
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
350 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
351
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
352 The available modes are::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
353
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
354 --mode {conservative,normal,bold}
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
355 Bridging mode (default: normal)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
356 conservative = smaller contigs, lowest misassembly rate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
357 normal = moderate contig size and misassembly rate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
358 bold = longest contigs, higher misassembly rate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
359
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
360 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
361
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
362 **Skip SPAdes error correction step**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
363
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
364 Sequencing data contains a substantial number of sequencing errors that manifest themselves as deviations (bulges and non-connected components) within the assembly graph. One of the ways to improve the graph even constructing it is to minimize the amount sequencing errors by performing error correction. SPAdes, which is used by Unicycler for error correction and assembly, uses `BayesHammer`_ to correct the reads. Here is a brief summary of what it does:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
365
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
366 1. SPAdes (or rather BayesHammer) counts *k*-mers in reads and computed *k*-mer statistics that takes into account base quality values.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
367 2. `Hamming graph`_ is constructed for *k*-mers is which *k*-mers are nodes. In this graph edges connect nodes (*k*-mers) is they differ from each other by a number of nucleotides up to a certain threshold (the `Hamming distance`_). The graph is central to the error correction algorithm.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
368 3. At this step Bayesian subclustering of the graph produced in the previous step. For each *k*-mer we now know the center of its subcluster.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
369 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
370 5. Solid *k*-mers are mapped back to the reads and used to correct them.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
371
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
372 This step takes considerable time, so if one need to quickly evaluate assemblies this step can be skipped. However, this is not recommended if one if trying to produce a final high quality assembly.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
373
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
374 .. _`BayesHammer`: https://goo.gl/1iGkMe
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
375 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
376 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
377
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
378 This following option turns error correction on and off::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
379
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
380 --no_correct
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
381 Skip SPAdes error correction step
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
382 (default: conduct SPAdes error correction)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
383
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
384 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
385
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
386 **Do not rotate completed replicons to start at a standard gene**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
387
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
388 Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
389
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
390 The following option turns rotation on and off::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
391
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
392 --no_rotate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
393 Do not rotate completed replicons
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
394 to start at a standard gene
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
395 (default: completed replicons are rotated)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
396
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
397 **Do not use Pilon to polish the final assembly**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
398
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
399 `Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly *polishing*.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
400
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
401 The following option turns pilon part of Unicycler pipeline on and off::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
402
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
403 --no_pilon
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
404 Do not use Pilon to polish the
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
405 final assembly (default: Pilon is used)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
406
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
407 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
408
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
409 ------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
410
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
411 **Expected number of linear sequences**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
412
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
413 If you expect your sample to contain linear (non circular) sequences, set this option::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
414
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
415 --linear_seqs EXPECTED_LINEAR_SEQS
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
416 The expected number of linear (i.e. non-circular)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
417 sequences in the underlying sequence
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
418
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
419 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
420
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
421 **SPAdes options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
422
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
423 This section provides control of SPAdes options::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
424
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
425 --min_kmer_frac MIN_KMER_FRAC
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
426 Lowest k-mer size for SPAdes assembly,
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
427 expressed as a fraction of the read length
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
428 (default: 0.2)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
429 --max_kmer_frac MAX_KMER_FRAC
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
430 Highest k-mer size for SPAdes assembly,
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
431 expressed as a fraction of the read length
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
432 (default: 0.95)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
433 --kmer_count KMER_COUNT
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
434 Number of k-mer steps to use in
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
435 SPAdes assembly (default: 10)
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
436 --depth_filter DEPTH_FILTER
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
437 Filter out contigs lower than this fraction
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
438 of the chromosomal depth, if doing so does
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
439 not result in graph dead ends (default: 0.25)
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
440
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
441 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
442
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
443 **Rotation options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
444
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
445 Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
446
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
447 --start_genes START_GENES
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
448 FASTA file of genes for start point
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
449 of rotated replicons
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
450 (default: start_genes.fasta)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
451 --start_gene_id START_GENE_ID
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
452 The minimum required BLAST percent identity
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
453 for a start gene search
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
454 (default: 90.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
455 --start_gene_cov START_GENE_COV
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
456 The minimum required BLAST percent coverage
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
457 for a start gene search
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
458 (default: 95.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
459
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
460 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
461
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
462 **Graph cleaning options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
463
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
464 These options control the removal of small leftover sequences after bridging is complete::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
465
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
466 --min_component_size MIN_COMPONENT_SIZE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
467 Unbridged graph components smaller
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
468 than this size (bp) will be removed
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
469 from the final graph (default: 1000)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
470 --min_dead_end_size MIN_DEAD_END_SIZE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
471 Graph dead ends smaller than this size (bp)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
472 will be removed from the final graph
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
473 (default: 1000)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
474
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
475 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
476
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
477 **Long read alignment options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
478
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
479 These options control the alignment of long reads to the assembly graph::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
480
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
481 --contamination CONTAMINATION
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
482 FASTA file of known contamination in long reads
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
483 --scores SCORES
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
484 Comma-delimited string of alignment scores:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
485 match, mismatch, gap open, gap extend
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
486 (default: 3,-6,-5,-2)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
487 --low_score LOW_SCORE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
488 Score threshold - alignments below this
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
489 are considered poor
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
490 (default: set threshold automatically)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
491
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
492 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
493
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
494 **Outputs**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
495
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
496 Galaxy's wrapped for Unicycler produces two outputs:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
497
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
498 * final assembly in FASTA format
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
499 * final assembly grapth in graph format
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
500
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
501 While most will likely be interested in the FASTA dataset, the graph dataset is also quite useful and can be visualized using tools such as `Bandage`_.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
502
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
503
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
504 .. _`Bandage`: https://github.com/rrwick/Bandage
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
505
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
506
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
507 ]]></help>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
508 <citations>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
509 <citation type="doi">10.1101/096412</citation>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
510 </citations>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
511 </tool>