Mercurial > repos > iuc > unicycler
annotate unicycler.xml @ 10:d10bdad2fd17 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
| author | iuc |
|---|---|
| date | Fri, 21 Oct 2022 16:02:46 +0000 |
| parents | 6e26c9afd301 |
| children | 8f9f06995f98 |
| rev | line source |
|---|---|
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
2 <description>pipeline for bacterial genomes</description> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
3 <macros> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
4 <token name="@TOOL_VERSION@">0.5.0</token> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
5 <token name="@VERSION_SUFFIX@">1</token> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
6 </macros> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
7 <xrefs> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
8 <xref type="bio.tools">unicycler</xref> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
9 </xrefs> |
|
7
88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
|
10 <edam_topics> |
|
88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
|
11 <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
|
12 </edam_topics> |
|
88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
|
13 <edam_operations> |
|
88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
|
14 <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
|
15 </edam_operations> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
16 <requirements> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
17 <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
18 <requirement type="package" version="1.15.1">samtools</requirement> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
19 </requirements> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
20 <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
|
21 ## Preparing files |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
22 #set $uncompressed = ('fastqsanger','fastq') |
|
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
23 #set $compressed = ('fastqsanger.gz','fastq.gz') |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
24 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
25 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
26 #set fq1 = "fq1.fastq" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
27 #elif $paired_unpaired.fastq_input1.file_ext in $compressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
28 #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
|
29 #end if |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
30 #if $paired_unpaired.fastq_input2.file_ext in $uncompressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
31 #set fq2 = "fq2.fastq" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
32 #elif $paired_unpaired.fastq_input2.file_ext in $compressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
33 #set fq2 = "fq2.fastq.gz" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
34 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
35 ln -s '${paired_unpaired.fastq_input1}' $fq1 && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
36 ln -s '${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
|
37 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
38 #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
39 #set fq1 = "fq1.fastq" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
40 #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
41 #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
|
42 #end if |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
43 #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
44 #set fq2 = "fq2.fastq" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
45 #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
46 #set fq2 = "fq2.fastq.gz" |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
47 #end if |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
48 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
49 ln -s '${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
|
50 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
51 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
52 #set fq = "fq.fastq" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
53 #elif $paired_unpaired.fastq_input1.file_ext in $compressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
54 #set fq = "fq.fastq.gz" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
55 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
56 ln -s '${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
|
57 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
58 #if $long |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
59 #if $long.file_ext in $uncompressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
60 #set lr = "lr.fastq" |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
61 #elif $long.file_ext in $compressed |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
62 #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
|
63 #elif $long.is_of_type('fasta') |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
64 #set lr = "lr.fasta" |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
65 #end if |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
66 ln -s '${long}' '$lr' && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
67 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
68 ## Running Unicycler |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
69 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
|
70 -o ./ |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
71 --verbosity 3 |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
72 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
73 -1 '$fq1' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
74 -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
|
75 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
76 -1 '$fq1' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
77 -2 '$fq2' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
78 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
79 -s '$fq' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
80 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
81 #if $long |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
82 -l $lr |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
83 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
84 ## General Unicycler Options section |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
85 ## ---------------------------------------------------------- |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
86 --mode '$mode' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
87 --min_fasta_length '$min_fasta_length' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
88 --linear_seqs '$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
|
89 #if str($min_anchor_seg_len) != '' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
90 --min_anchor_seg_len '$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
|
91 #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
|
92 ## 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
|
93 ## ---------------------------------------------------------- |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
94 --min_kmer_frac '$spades.min_kmer_frac' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
95 --max_kmer_frac '$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
|
96 #if str($spades.kmers) != '' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
97 --kmers '$spades.kmers' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
98 #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
|
99 --kmer_count '$spades.kmer_count' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
100 --depth_filter '$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
|
101 #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
|
102 --largest_component |
|
88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
|
103 #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
|
104 ## 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
|
105 ## ---------------------------------------------------------- |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
106 $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
|
107 #if $rotation.start_genes |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
108 --start_genes '$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
|
109 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
110 --start_gene_id '$rotation.start_gene_id' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
111 --start_gene_cov '$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
|
112 ## 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
|
113 ## ---------------------------------------------------------- |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
114 --min_component_size '$graph_clean.min_component_size' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
115 --min_dead_end_size '$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
|
116 ## 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
|
117 ## ---------------------------------------------------------- |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
118 #if $lr_align.contamination |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
119 --contamination '$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
|
120 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
121 --scores '${lr_align.scores}' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
122 #if str($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
|
123 --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
|
124 #end if |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
125 $lr_align.no_simple_bridges |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
126 --keep $keep |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
127 #if $keep != '0' |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
128 && mkdir 'spades_graphs' |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
129 && mv 00*gfa './spades_graphs/' |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
130 #end if |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
131 #if $keep == '2' and $long |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
132 && samtools view -@ "\${GALAXY_SLOTS:-4}" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o 'read_alignment/long_read_alignments.bam' |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
133 #end if |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
134 ]]></command> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
135 <inputs> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
136 <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
|
137 <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
|
138 <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
|
139 <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
|
140 <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
|
141 <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
|
142 </param> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
143 <when value="paired"> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
144 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
|
6
0a3a602cd1e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents:
5
diff
changeset
|
145 label="Select first set of reads" help="Specify dataset with forward reads"/> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
146 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
|
6
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 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
|
148 </when> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
149 <when value="paired_collection"> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
150 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
151 </when> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
152 <when value="single"> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
153 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
|
6
0a3a602cd1e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents:
5
diff
changeset
|
154 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
|
155 </when> |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
156 <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
|
157 </when> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
158 </conditional> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
|
159 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta,fastq,fastq.gz" label="Select long reads. If there are no long reads, leave this empty"/> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
160 <param argument="--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
|
161 <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
|
162 <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
|
163 <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
|
164 </param> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
165 <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
|
166 <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
|
167 <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
|
168 <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
|
169 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
|
170 <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
|
171 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
|
172 <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
|
173 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
|
174 <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
|
175 <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
|
176 </param> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
177 <param 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
|
178 <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
|
179 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
|
180 <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
|
181 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
|
182 </section> |
|
6
0a3a602cd1e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
parents:
5
diff
changeset
|
183 <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
|
184 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
|
185 <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
|
186 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
|
187 <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
|
188 <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
|
189 <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
|
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"/> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
204 <param argument="--no_simple_bridges" type="boolean" truevalue="--no_simple_bridges" falsevalue="" checked="false" label="Simple long-read bridging" help="Default: No" /> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
205 </section> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
206 <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
207 <option value="0">0: only keep final files</option> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
208 <option value="1" selected="true">1: save graphs at main checkpoints</option> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
209 <option value="2">2: also keep SAM</option> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
210 </param> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
211 </inputs> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
212 <outputs> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
213 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
214 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
215 <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
216 <discover_datasets pattern="__designation_and_ext__" format="gfa1" directory="spades_graphs"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
217 <filter>keep != "0"</filter> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
218 </collection> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
219 <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
220 <filter>keep == "2" and long</filter> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
221 </data> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
222 </outputs> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
223 <tests> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
224 <test expect_num_outputs="2"> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
225 <conditional name="paired_unpaired"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
226 <param name="fastq_input_selector" value="paired" /> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
227 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
228 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
229 </conditional> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
230 <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
|
231 <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
|
232 <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
|
233 <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
|
234 <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
|
235 <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
|
236 <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
|
237 <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
|
238 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
239 <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
|
240 <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
|
241 <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
|
242 <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
|
243 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
244 <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
|
245 <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
|
246 <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
|
247 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
248 <section name="lr_align"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
249 <param name="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
|
250 </section> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
251 <param name="keep" value="0"/> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
252 <output name="assembly_graph" ftype="gfa1"> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
253 <assert_contents> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
254 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
255 </assert_contents> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
256 </output> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
257 <output name="assembly" ftype="fasta"> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
258 <assert_contents> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
259 <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
|
260 </assert_contents> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
261 </output> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
262 </test> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
263 <!-- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
264 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
|
265 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
266 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
|
267 -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
|
268 - -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
|
269 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
270 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
|
271 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
|
272 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
|
273 --> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
274 <test expect_num_outputs="2"> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
275 <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
|
276 <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
|
277 <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
|
278 <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
|
279 </conditional> |
|
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="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
|
281 <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
|
282 <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
|
283 <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
|
284 <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
|
285 <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
|
286 <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
|
287 <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
|
288 <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
|
289 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
290 <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
|
291 <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
|
292 <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
|
293 <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
|
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="graph_clean"> |
|
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="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
|
297 <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
|
298 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
299 <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
|
300 <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
|
301 </section> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
302 <param name="keep" value="0"/> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
303 <output name="assembly_graph" ftype="gfa1"> |
|
2
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> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
305 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
2
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 <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
|
309 <assert_contents> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
310 <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
|
311 </assert_contents> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
312 </output> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
313 </test> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
314 <test expect_num_outputs="2"> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
315 <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
|
316 <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
|
317 <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
|
318 <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
|
319 <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
|
320 <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
|
321 </collection> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
322 </param> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
323 </conditional> |
|
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="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
|
325 <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
|
326 <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
|
327 <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
|
328 <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
|
329 <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
|
330 <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
|
331 <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
|
332 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
333 <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
|
334 <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
|
335 <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
|
336 <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
|
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> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
345 <param name="keep" value="0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
346 <output name="assembly_graph" ftype="gfa1"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
347 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
348 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
349 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
350 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
351 <output name="assembly" ftype="fasta"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
352 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
353 <has_text text="length=5386" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
354 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
355 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
356 </test> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
357 <test expect_num_outputs="2"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
358 <conditional name="paired_unpaired"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
359 <param name="fastq_input_selector" value="none"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
360 </conditional> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
361 <param name="min_anchor_seg_len" value="10"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
362 <section name="spades"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
363 <param name="kmers" value="21,23"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
364 </section> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
365 <param name="long" value="only_long.fasta" ftype="fasta" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
366 <param name="keep" value="0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
367 <output name="assembly_graph" ftype="gfa1"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
368 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
369 <has_text text="S" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
370 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
371 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
372 <output name="assembly" ftype="fasta"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
373 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
374 <has_text text=">1" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
375 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
376 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
377 </test> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
378 <!-- Test keep value = 1 --> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
379 <test expect_num_outputs="3"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
380 <conditional name="paired_unpaired"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
381 <param name="fastq_input_selector" value="paired" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
382 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
383 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
384 </conditional> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
385 <param name="mode" value="normal" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
386 <param name="keep" value="1"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
387 <output name="assembly_graph" ftype="gfa1"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
388 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
389 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
390 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
391 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
392 <output name="assembly" ftype="fasta"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
393 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
394 <has_text text="length=5386" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
395 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
396 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
397 <output_collection name="spades_collection" type="list" count="14"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
398 <element name="001_spades_graph_k027"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
399 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
400 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
401 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
402 </element> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
403 </output_collection> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
404 </test> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
405 <!-- Test keep value = 2 --> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
406 <test expect_num_outputs="4"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
407 <conditional name="paired_unpaired"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
408 <param name="fastq_input_selector" value="paired" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
409 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
410 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
411 </conditional> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
412 <param name="long" value="onp.fa" ftype="fasta" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
413 <param name="mode" value="normal" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
414 <param name="keep" value="2"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
415 <output name="assembly_graph" ftype="gfa1"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
416 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
417 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
418 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
419 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
420 <output name="assembly" ftype="fasta"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
421 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
422 <has_text text="length=5386" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
423 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
424 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
425 <output_collection name="spades_collection" type="list" count="14"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
426 <element name="001_spades_graph_k027"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
427 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
428 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
429 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
430 </element> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
431 </output_collection> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
432 <output name="bam_file" ftype="bam"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
433 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
434 <has_size value="2084" delta="100"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
435 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
436 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
437 </test> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
438 <!-- Test no simple bridges option --> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
439 <test expect_num_outputs="2"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
440 <conditional name="paired_unpaired"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
441 <param name="fastq_input_selector" value="paired" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
442 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
443 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
444 </conditional> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
445 <param name="long" value="onp.fa" ftype="fasta" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
446 <param name="mode" value="normal" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
447 <param name="keep" value="0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
448 <section name="lr_align"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
449 <param name="no_simple_bridges" value="true"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
450 </section> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
451 <output name="assembly_graph" ftype="gfa1"> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
452 <assert_contents> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
453 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
454 </assert_contents> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
455 </output> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
456 <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
|
457 <assert_contents> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
458 <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
|
459 </assert_contents> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
460 </output> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
461 <assert_command> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
462 <has_text text="--no_simple_bridges" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
463 </assert_command> |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
464 </test> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
465 </tests> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
466 <help><![CDATA[ |
|
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 **Unicycler** |
|
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 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
|
471 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
472 .. _`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
|
473 .. _`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
|
474 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
475 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
476 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
477 **Input data** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
478 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
479 Unicycler 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
|
480 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
481 .. _`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
|
482 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
483 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
|
484 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
485 -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
|
486 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
|
487 -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
|
488 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
|
489 -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
|
490 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
|
491 -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
|
492 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
|
493 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
494 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
495 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
496 **Bridging mode** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
497 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
498 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
|
499 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
500 .. _`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
|
501 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
502 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
|
503 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
504 --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
|
505 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
|
506 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
|
507 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
|
508 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
|
509 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
510 ---- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
511 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
512 **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
|
513 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
514 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
|
515 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
516 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
|
517 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
|
518 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
|
519 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
|
520 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
|
521 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
522 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
|
523 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
524 .. _`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
|
525 .. _`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
|
526 .. _`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
|
527 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
528 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
529 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
530 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
531 **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
|
532 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
533 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
|
534 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
535 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
|
536 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
537 --no_rotate |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
538 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
|
539 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
|
540 (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
|
541 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
542 **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
|
543 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
544 `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
|
545 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
546 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
|
547 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
548 --no_pilon |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
549 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
|
550 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
|
551 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
552 .. _`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
|
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 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
556 **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
|
557 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
558 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
|
559 |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
560 --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
|
561 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
|
562 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
|
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 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
566 **SPAdes options** |
|
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 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
|
569 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
570 --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
|
571 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
|
572 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
|
573 (default: 0.2) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
574 --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
|
575 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
|
576 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
|
577 (default: 0.95) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
578 --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
|
579 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
|
580 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
|
581 --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
|
582 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
|
583 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
|
584 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
|
585 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
586 ---- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
587 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
588 **Rotation options** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
589 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
590 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
|
591 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
592 --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
|
593 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
|
594 of rotated replicons |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
595 (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
|
596 --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
|
597 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
|
598 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
|
599 (default: 90.0) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
600 --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
|
601 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
|
602 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
|
603 (default: 95.0) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
604 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
605 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
606 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
607 **Graph cleaning options** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
608 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
609 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
|
610 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
611 --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
|
612 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
|
613 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
|
614 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
|
615 --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
|
616 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
|
617 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
|
618 (default: 1000) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
619 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
620 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
621 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
622 **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
|
623 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
624 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
|
625 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
626 --contamination CONTAMINATION |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
627 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
|
628 --scores SCORES |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
629 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
|
630 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
|
631 (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
|
632 --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
|
633 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
|
634 are considered poor |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
635 (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
|
636 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
637 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
638 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
639 **Outputs** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
640 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
641 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
|
642 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
643 * 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
|
644 * 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
|
645 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
646 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
|
647 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
648 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
649 .. _`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
|
650 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
651 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
652 ]]></help> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
653 <citations> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
654 <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
|
655 </citations> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
656 </tool> |