annotate unicycler.xml @ 5:23300b42ca18 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
author iuc
date Wed, 19 Sep 2018 17:07:02 -0400
parents 2db911a4efc5
children 0a3a602cd1e3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
c4eac0c7e542 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 10ded2007c3502079b28afcef4718c430755e9b8
iuc
parents: 2
diff changeset
1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0">
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
2 <macros>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
3 <token name="@VERSION@">0.4.6</token>
2
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>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
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
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
61 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
62 -1 '$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'
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
64 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
65 -1 '$fq1'
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
66 -2 '$fq2'
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
67 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
68 -s '$fq'
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 #if $long
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
71 -l $lr
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
72 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
73 ## General Unicycler Options section
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
74 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
75 --mode '$mode'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
76 --min_fasta_length '$min_fasta_length'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
77 --linear_seqs '$linear_seqs'
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
78 #if str($min_anchor_seg_len) != ''
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
79 --min_anchor_seg_len '$min_anchor_seg_len'
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
80 #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
81 ## 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
82 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
83 $spades.no_correct
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
84 --min_kmer_frac '$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
85 --max_kmer_frac '$spades.max_kmer_frac'
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
86 #if str($spades.kmers) != ''
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
87 --kmers '$spades.kmers'
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
88 #end if
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
89 --kmer_count '$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
90 --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
91 ## 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
92 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
93 $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
94 #if $rotation.start_genes
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
95 --start_genes '$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
96 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
97 --start_gene_id '$rotation.start_gene_id'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
98 --start_gene_cov '$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
99 ## 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
100 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
101 $pilon.no_pilon
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
102 #if str($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
103 --min_polish_size '$pilon.min_polish_size'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
104 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
105 ## Graph cleaning Options sdection
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
106 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
107 --min_component_size '$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
108 --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
109 ## 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
110 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
111 #if $lr_align.contamination
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
112 --contamination '$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
113 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
114 --scores '${lr_align.scores}'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
115 #if str($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
116 --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
117 #end if
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
118 ]]></command>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
119 <inputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
120 <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
121 <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
122 <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
123 <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
124 <option value="single">Single</option>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
125 <option value="none">None</option>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
126 </param>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
127 <when value="paired">
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
128 <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
129 <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
130 </when>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
131 <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
132 <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
133 </when>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
134 <when value="single">
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
135 <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
136 </when>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
137 <when value="none">
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
138 </when>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
139 </conditional>
2
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="--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
141 <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
142 <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
143 <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
144 <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
145 </param>
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="--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
147 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
148 <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
149 <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
150 <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
151 <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
152 <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"/>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
153 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated">
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
154 <validator type="regex" message="Kmers must be comma-separated odd integers (no repitition) without space in the range of 11 to 127 (inclusive)">^(\d*[13579],)*(\d*[13579])$</validator>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
155 </param>
2
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="--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
157 <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
158 </section>
2
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="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
160 <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
161 <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
162 <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
163 <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
164 </section>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
165 <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
166 <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
167 <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
168 </section>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
169 <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
170 <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
171 <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
172 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
173 <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
174 <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
175 <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
176 <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
177 </section>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
178 </inputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
179 <outputs>
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
180 <data name="assembly_graph" format="tabular" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
181 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${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
182 </outputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
183 <tests>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
184 <test>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
185 <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
186 <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
187 <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
188 <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
189 </conditional>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
190 <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
191 <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
192 <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
193 <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
194 <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
195 <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
196 <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
197 <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
198 <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
199 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
200 <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
201 <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
202 <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
203 <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
204 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
205 <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
206 <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
207 <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
208 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
209 <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
210 <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
211 <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
212 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
213 <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
214 <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
215 </section>
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
216 <output name="assembly_graph" ftype="tabular">
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
217 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
218 <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
219 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
220 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
221 <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
222 <assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
223 <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
224 </assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
225 </output>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
226 </test>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
227 <!--
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
228 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
229
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
230 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
231 -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
232 - -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
233
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
234 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
235 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
236 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
237 -->
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
238 <test>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
239 <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
240 <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
241 <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
242 <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
243 </conditional>
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="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
245 <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
246 <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
247 <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
248 <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
249 <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
250 <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
251 <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
252 <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
253 <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
254 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
255 <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
256 <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
257 <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
258 <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
259 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
260 <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
261 <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
262 <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
263 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
264 <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
265 <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
266 <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
267 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
268 <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
269 <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
270 </section>
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
271 <output name="assembly_graph" ftype="tabular">
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
272 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
273 <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
274 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
275 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
276 <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
277 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
278 <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
279 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
280 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
281 </test>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
282 <test>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
283 <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
284 <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
285 <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
286 <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
287 <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
288 <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
289 </collection>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
290 </param>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
291 </conditional>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
292 <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
293 <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
294 <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
295 <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
296 <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
297 <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
298 <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
299 <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
300 <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
301 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
302 <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
303 <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
304 <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
305 <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
306 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
307 <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
308 <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
309 <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
310 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
311 <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
312 <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
313 <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
314 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
315 <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
316 <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
317 </section>
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
318 <output name="assembly_graph" ftype="tabular">
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
319 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
320 <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
321 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
322 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
323 <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
324 <assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
325 <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
326 </assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
327 </output>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
328 </test>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
329 <test>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
330 <conditional name="paired_unpaired">
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
331 <param name="fastq_input_selector" value="none"/>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
332 </conditional>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
333 <param name="min_anchor_seg_len" value="10"/>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
334 <section name="spades">
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
335 <param name="kmers" value="21,23"/>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
336 </section>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
337 <param name="long" value="only_long.fasta" ftype="fasta" />
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
338 <output name="assembly_graph" ftype="tabular">
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
339 <assert_contents>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
340 <has_text text="S" />
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
341 </assert_contents>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
342 </output>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
343 <output name="assembly" ftype="fasta">
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
344 <assert_contents>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
345 <has_text text=">1" />
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
346 </assert_contents>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
347 </output>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
348 </test>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
349 </tests>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
350 <help><![CDATA[
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 **Unicycler**
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 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
355
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
356 .. _`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
357 .. _`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
358
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 **Input data**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
362
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
363 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
364
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
365 .. _`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
366
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
367 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
368
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
369 -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
370 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
371 -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
372 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
373 -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
374 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
375 -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
376 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
377
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
378 -----
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 **Bridging mode**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
381
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
382 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
383
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
384 .. _`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
385
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
386 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
387
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
388 --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
389 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
390 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
391 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
392 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
393
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
394 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
395
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
396 **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
397
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
398 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
399
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
400 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
401 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
402 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
403 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
404 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
405
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
406 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
407
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
408 .. _`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
409 .. _`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
410 .. _`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
411
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
412 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
413
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
414 --no_correct
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
415 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
416 (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
417
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 **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
421
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
422 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
423
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
424 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
425
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
426 --no_rotate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
427 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
428 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
429 (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
430
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
431 **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
432
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
433 `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
434
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
435 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
436
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
437 --no_pilon
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
438 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
439 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
440
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
441 .. _`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
442
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
443 ------
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 **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
446
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
447 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
448
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
449 --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
450 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
451 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
452
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
453 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
454
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
455 **SPAdes options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
456
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
457 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
458
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
459 --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
460 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
461 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
462 (default: 0.2)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
463 --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
464 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
465 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
466 (default: 0.95)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
467 --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
468 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
469 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
470 --depth_filter DEPTH_FILTER
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
471 Filter out contigs lower than this fraction
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
472 of the chromosomal depth, if doing so does
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
473 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
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 **Rotation 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 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
480
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
481 --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
482 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
483 of rotated replicons
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
484 (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
485 --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
486 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
487 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
488 (default: 90.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
489 --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
490 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
491 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
492 (default: 95.0)
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 -----
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 **Graph cleaning options**
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 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
499
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
500 --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
501 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
502 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
503 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
504 --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
505 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
506 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
507 (default: 1000)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
508
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
509 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
510
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
511 **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
512
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
513 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
514
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
515 --contamination CONTAMINATION
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
516 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
517 --scores SCORES
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
518 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
519 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
520 (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
521 --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
522 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
523 are considered poor
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
524 (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
525
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
526 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
527
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
528 **Outputs**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
529
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
530 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
531
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
532 * 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
533 * 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
534
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
535 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
536
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
537
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
538 .. _`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
539
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
540
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
541 ]]></help>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
542 <citations>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
543 <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
544 </citations>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
545 </tool>