Mercurial > repos > iuc > unicycler

annotate unicycler.xml @ 7:88c240872a65 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
author iuc
date Tue, 08 Oct 2019 02:47:44 -0400
parents 0a3a602cd1e3
children 9e3e80cc4ad4
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>
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
3 <token name="@VERSION@">0.4.8</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>
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
5 <edam_topics>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
6 <edam_topic>topic_0196</edam_topic>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
7 </edam_topics>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
8 <edam_operations>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
9 <edam_operation>operation_0525</edam_operation>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
10 </edam_operations>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
11 <requirements>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
12 <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
13 </requirements>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
14 <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
15 ## Preparing files
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
16 #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
17 #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
18 #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
19 #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
20 #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
21 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
22 #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
23 #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
24 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
25 #set fq2 = "fq2.fastq.gz"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
26 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
27 ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
28 ln -s '${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
29 #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
30 #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
31 #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
32 #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
33 #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
34 #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
35 #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
36 #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
37 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
38 #set fq2 = "fq2.fastq.gz"
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
39 #end if
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
40 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
41 ln -s '${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
42 #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
43 #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
44 #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
45 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
46 #set fq = "fq.fastq.gz"
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
47 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
48 ln -s '${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
49 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
50 #if $long
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
51 #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
52 #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
53 #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
54 #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
55 #elif $long.is_of_type('fasta')
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
56 #set lr = "lr.fasta"
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
57 #end if
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
58 ln -s '${long}' '$lr' &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
59 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
60 ## 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
61 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
62 ## Running Unicycler
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
63 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
64 -o ./
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
65 --verbosity 3
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
66 --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
67 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
68 -1 '$fq1'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
69 -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
70 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
71 -1 '$fq1'
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
72 -2 '$fq2'
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
73 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
74 -s '$fq'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
75 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
76 #if $long
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
77 -l $lr
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
78 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
79 ## General Unicycler Options section
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
80 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
81 --mode '$mode'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
82 --min_fasta_length '$min_fasta_length'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
83 --linear_seqs '$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
84 #if str($min_anchor_seg_len) != ''
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
85 --min_anchor_seg_len '$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
86 #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
87 ## 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
88 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
89 $spades.no_correct
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
90 --min_kmer_frac '$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
91 --max_kmer_frac '$spades.max_kmer_frac'
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
92 #if str($spades.kmers) != ''
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
93 --kmers '$spades.kmers'
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
94 #end if
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
95 --kmer_count '$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
96 --depth_filter '$spades.depth_filter'
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
97 #if $spades.largest_component
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
98 --largest_component
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
99 #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
100 ## 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
101 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
102 $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
103 #if $rotation.start_genes
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
104 --start_genes '$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
105 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
106 --start_gene_id '$rotation.start_gene_id'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
107 --start_gene_cov '$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
108 ## 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
109 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
110 $pilon.no_pilon
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
111 #if str($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
112 --min_polish_size '$pilon.min_polish_size'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
113 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
114 ## Graph cleaning Options sdection
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
115 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
116 --min_component_size '$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
117 --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
118 ## 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
119 ## ----------------------------------------------------------
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
120 #if $lr_align.contamination
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
121 --contamination '$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
122 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
123 --scores '${lr_align.scores}'
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
124 #if str($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
125 --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
126 #end if
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
127 ]]></command>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
128 <inputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
129 <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
130 <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
131 <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
132 <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
133 <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
134 <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
135 </param>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
136 <when value="paired">
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
137 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
138 label="Select first set of reads" help="Specify dataset with forward reads"/>
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
139 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
140 label="Select second set of reads" help="Specify dataset with reverse reads"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
141 </when>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
142 <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
143 <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
144 </when>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
145 <when value="single">
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
146 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
147 label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
148 </when>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
149 <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
150 </when>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
151 </conditional>
2
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="--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
153 <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
154 <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
155 <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
156 <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
157 </param>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
158 <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
159 <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
160 <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/>
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
161 <section name="spades" expanded="False" title="SPAdes options"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
162 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!">
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
163 <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue=""
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
164 label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
165 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
166 label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
167 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
168 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
169 <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
170 <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
171 </param>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
172 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
173 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
174 label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/>
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
175 <param argument="--largest_component" type="boolean" checked="false"
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
176 label="Only keep the largest connected component of the assembly graph"/>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
177 </section>
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
178 <section name="rotation" expanded="false" title="Rotation options"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
179 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!">
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
180 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue=""
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
181 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."/>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
182 <param 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
183 <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
184 <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
185 </section>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
186 <section name="pilon" title="Pilon options" expanded="false">
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
187 <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue=""
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
188 label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
189 <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
190 </section>
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
191 <section name="graph_clean" expanded="false" title="Graph cleaning options"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
192 help="These options control the removal of small leftover sequences after bridging is complete.">
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
193 <param argument="--min_component_size" type="integer" min="0" value="1000"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
194 label="Unbridged graph components smaller than this size will be removed from the final graph" />
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
195 <param argument="--min_dead_end_size" type="integer" min="0" value="1000"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
196 label="Graph dead ends smaller than this size will be removed from the final graph"/>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
197 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
198 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
199 <param argument="--contamination" optional="true" type="data" format="fasta"
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
200 label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
201 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>
6
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
202 <param argument="--low_score" optional="true" type="integer" value=""
0a3a602cd1e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents: 5
diff changeset
203 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
204 </section>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
205 </inputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
206 <outputs>
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
207 <data name="assembly_graph" format="tabular" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
208 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${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
209 </outputs>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
210 <tests>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
211 <test>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
212 <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
213 <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
214 <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
215 <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
216 </conditional>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
217 <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
218 <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
219 <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
220 <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
221 <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
222 <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
223 <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
224 <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
225 <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
226 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
227 <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
228 <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
229 <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
230 <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
231 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
232 <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
233 <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
234 <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
235 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
236 <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
237 <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
238 <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
239 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
240 <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
241 <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
242 </section>
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
243 <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
244 <assert_contents>
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
245 <has_text text="TATCTGTTACTGAGAAGTTAATGGATGAATTGGCAC"/>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
246 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
247 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
248 <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
249 <assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
250 <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
251 </assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
252 </output>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
253 </test>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
254 <!--
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
255 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
256
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
257 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
258 -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
259 - -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
260
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
261 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
262 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
263 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
264 -->
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
265 <test>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
266 <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
267 <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
268 <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
269 <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
270 </conditional>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
271 <param name="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
272 <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
273 <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
274 <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
275 <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
276 <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
277 <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
278 <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
279 <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
280 <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
281 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
282 <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
283 <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
284 <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
285 <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
286 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
287 <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
288 <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
289 <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
290 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
291 <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
292 <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
293 <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
294 </section>
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="lr_align">
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="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
297 </section>
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
298 <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
299 <assert_contents>
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
300 <has_text text="TATCTGTTACTGAGAAGTTAATGGATGAATTGGCAC" />
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
301 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
302 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
303 <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
304 <assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
305 <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
306 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
307 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
308 </test>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
309 <test>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
310 <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
311 <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
312 <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
313 <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
314 <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
315 <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
316 </collection>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
317 </param>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
318 </conditional>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
319 <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
320 <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
321 <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
322 <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
323 <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
324 <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
325 <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
326 <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
327 <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
328 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
329 <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
330 <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
331 <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
332 <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
333 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
334 <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
335 <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
336 <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
337 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
338 <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
339 <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
340 <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
341 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
342 <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
343 <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
344 </section>
5
23300b42ca18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
iuc
parents: 4
diff changeset
345 <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
346 <assert_contents>
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
347 <has_text text="TATCTGTTACTGAGAAGTTAATGGATGAATTGGCAC" />
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
348 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
349 </output>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
350 <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
351 <assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
352 <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
353 </assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
354 </output>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
355 </test>
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
356 <test>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
357 <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
358 <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
359 </conditional>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
360 <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
361 <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
362 <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
363 </section>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
364 <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
365 <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
366 <assert_contents>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
367 <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
368 </assert_contents>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
369 </output>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
370 <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
371 <assert_contents>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
372 <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
373 </assert_contents>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
374 </output>
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
375 </test>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
376 </tests>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
377 <help><![CDATA[
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 **Unicycler**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
380
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
381 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
382
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
383 .. _`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
384 .. _`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
385
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
386 -----
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 **Input data**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
389
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
390 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
391
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
392 .. _`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
393
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
394 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
395
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
396 -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
397 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
398 -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
399 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
400 -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
401 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
402 -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
403 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
404
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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
407 **Bridging mode**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
408
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
409 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
410
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
411 .. _`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
412
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
413 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
414
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
415 --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
416 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
417 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
418 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
419 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
420
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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
423 **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
424
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
425 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
426
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
427 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
428 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
429 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
430 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
431 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
432
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
433 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
434
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
435 .. _`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
436 .. _`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
437 .. _`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
438
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
439 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
440
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
441 --no_correct
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
442 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
443 (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
444
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
445 -----
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 **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
448
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
449 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
450
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
451 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
452
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
453 --no_rotate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
454 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
455 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
456 (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
457
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
458 **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
459
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
460 `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
461
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
462 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
463
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
464 --no_pilon
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
465 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
466 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
467
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
468 .. _`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
469
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
470 ------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
471
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
472 **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
473
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
474 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
475
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
476 --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
477 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
478 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
479
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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
482 **SPAdes options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
483
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
484 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
485
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
486 --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
487 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
488 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
489 (default: 0.2)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
490 --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
491 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
492 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
493 (default: 0.95)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
494 --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
495 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
496 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
497 --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
498 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
499 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
500 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
501
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
502 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
503
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
504 **Rotation options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
505
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
506 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
507
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
508 --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
509 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
510 of rotated replicons
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
511 (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
512 --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
513 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
514 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
515 (default: 90.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
516 --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
517 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
518 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
519 (default: 95.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
520
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
521 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
522
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
523 **Graph cleaning options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
524
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
525 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
526
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
527 --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
528 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
529 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
530 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
531 --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
532 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
533 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
534 (default: 1000)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
535
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 **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
539
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
540 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
541
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
542 --contamination CONTAMINATION
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
543 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
544 --scores SCORES
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
545 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
546 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
547 (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
548 --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
549 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
550 are considered poor
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
551 (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
552
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
553 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
554
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
555 **Outputs**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
556
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
557 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
558
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
559 * 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
560 * 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
561
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
562 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
563
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
564
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
565 .. _`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
566
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
567
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
568 ]]></help>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
569 <citations>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
570 <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
571 </citations>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
572 </tool>