Mercurial > repos > devteam > bowtie2
annotate bowtie2_wrapper.xml @ 15:7e0b333f39e1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
| author | iuc |
|---|---|
| date | Thu, 01 Jun 2017 06:46:49 -0400 |
| parents | 85f0e9edb32d |
| children | def46fdb3909 |
| rev | line source |
|---|---|
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1 <tool id="bowtie2" name="Bowtie2" version="2.3.2.1" profile="17.01"> |
| 2 | 2 <description>- map reads against reference genome</description> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
3 <macros> |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
4 <import>bowtie2_macros.xml</import> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
5 </macros> |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
6 <requirements> |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
7 <requirement type="package" version="2.3.2">bowtie2</requirement> |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
8 <requirement type="package" version="1.3.1">samtools</requirement> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
9 </requirements> |
| 0 | 10 <version_command>bowtie2 --version</version_command> |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
11 <command detect_errors="exit_code"><![CDATA[ |
| 0 | 12 ## prepare bowtie2 index |
| 13 #set index_path = '' | |
| 14 #if str($reference_genome.source) == "history": | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome && |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
16 ln -s -f '$reference_genome.own_file' genome.fa && |
| 0 | 17 #set index_path = 'genome' |
| 18 #else: | |
|
13
55dcd6aad1ab
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit b22fc2e7243522b264f3d5d00706df8d18366405
devteam
parents:
12
diff
changeset
|
19 #set index_path = $reference_genome.index.fields.path |
| 0 | 20 #end if |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
21 |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
22 ## Link in the input files, so bowtie2 can tell their type |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
23 |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
24 #set compressed="False" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
25 #if str($library.type) == 'paired': |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
26 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
27 #set read1 = "input_f.fastq.gz" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
28 #set compressed = "GZ" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
29 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
30 #set read1 = "input_f.fastq.bz2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
31 #set compressed = "BZ2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
32 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
33 #set read1 = "input_f.fastq" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
34 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
35 ln -f -s '${library.input_1}' ${read1} && |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
36 |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
37 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
38 #set read2 = "input_r.fastq.gz" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
39 #set compressed = "GZ" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
40 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
41 #set read2 = "input_r.fastq.bz2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
42 #set compressed = "BZ2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
43 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
44 #set read2 = "input_r.fastq" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
45 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
46 ln -f -s '${library.input_2}' ${read2} && |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
47 #else if str($library.type) == 'paired_collection': |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
48 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
49 #set read1 = "input_f.fastq.gz" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
50 #set compressed = "GZ" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
51 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
52 #set read1 = "input_f.fastq.bz2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
53 #set compressed = "BZ2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
54 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
55 #set read1 = "input_f.fastq" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
56 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
57 ln -s '${library.input_1.forward}' ${read1} && |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
58 |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
59 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
60 #set read2 = "input_r.fastq.gz" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
61 #set compressed = "GZ" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
62 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
63 #set read2 = "input_r.fastq.bz2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
64 #set compressed = "BZ2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
65 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
66 #set read2 = "input_r.fastq" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
67 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
68 ln -s '${library.input_1.reverse}' ${read2} && |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
69 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
70 #else if str($library.type) == 'paired_interleaved': |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
71 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
72 #set read1 = "input_il.fastq.gz" |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
73 #set compressed = "GZ" |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
74 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
75 #set read1 = "input_il.fastq.bz2" |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
76 #set compressed = "BZ2" |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
77 #else: |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
78 #set read1 = "input_il.fastq" |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
79 #end if |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
80 ln -s '${library.input_1}' ${read1} && |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
81 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
82 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
83 #set read1 = "input_f.fastq.gz" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
84 #set compressed = "GZ" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
85 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
86 #set read1 = "input_f.fastq.bz2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
87 #set compressed = "BZ2" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
88 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
89 #set read1 = "input_f.fastq" |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
90 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
91 ln -s '${library.input_1}' ${read1} && |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
92 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
93 |
| 0 | 94 ## execute bowtie2 |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
95 |
| 0 | 96 bowtie2 |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
97 |
| 0 | 98 ## number of threads |
| 99 -p \${GALAXY_SLOTS:-4} | |
| 100 | |
| 101 ## index file path | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
102 -x '$index_path' |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
103 |
| 2 | 104 ## Fastq inputs |
| 105 #if str( $library.type ) == "single": | |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
106 -U '${read1}' |
| 2 | 107 #if str( $library.unaligned_file ) == "true": |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
108 #if $compressed == "GZ": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
109 --un-gz '${output_unaligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
110 #else if $compressed == "BZ2": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
111 --un-bz2 '${output_unaligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
112 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
113 --un '${output_unaligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
114 #end if |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
115 #end if |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
116 #if str( $library.aligned_file ) == "true": |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
117 #if $compressed == "GZ": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
118 --al-gz '${output_aligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
119 #else if $compressed == "BZ2": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
120 --al-bz2 '${output_aligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
121 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
122 --al '${output_aligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
123 #end if |
| 0 | 124 #end if |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
125 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
126 #elif str( $library.type ) == "paired_interleaved": |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
127 --interleaved '${read1}' |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
128 #if str( $library.unaligned_file ) == "true": |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
129 #if $compressed == "GZ": |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
130 --un-gz '${output_unaligned_reads_l}' |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
131 #else if $compressed == "BZ2": |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
132 --un-bz2 '${output_unaligned_reads_l}' |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
133 #else: |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
134 --un '${output_unaligned_reads_l}' |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
135 #end if |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
136 #end if |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
137 #if str( $library.aligned_file ) == "true": |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
138 #if $compressed == "GZ": |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
139 --al-gz '${output_aligned_reads_l}' |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
140 #else if $compressed == "BZ2": |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
141 --al-bz2 '${output_aligned_reads_l}' |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
142 #else: |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
143 --al '${output_aligned_reads_l}' |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
144 #end if |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
145 #end if |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
146 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
147 -1 '${read1}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
148 -2 '${read2}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
149 #if str( $library.unaligned_file ) == "true": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
150 #if $compressed == "GZ": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
151 --un-conc-gz '${output_unaligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
152 #else if $compressed == "BZ2": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
153 --un-conc-bz2 '${output_unaligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
154 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
155 --un-conc '${output_unaligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
156 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
157 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
158 #if str( $library.aligned_file ) == "true": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
159 #if $compressed == "GZ": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
160 --al-conc-gz '${output_aligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
161 #else if $compressed == "BZ2": |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
162 --al-conc-bz2 '${output_aligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
163 #else: |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
164 --al-conc '${output_aligned_reads_l}' |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
165 #end if |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
166 #end if |
| 2 | 167 #if str( $library.paired_options.paired_options_selector ) == "yes": |
| 168 -I "${library.paired_options.I}" | |
| 169 -X "${library.paired_options.X}" | |
| 170 ${library.paired_options.fr_rf_ff} | |
| 171 ${library.paired_options.no_mixed} | |
| 172 ${library.paired_options.no_discordant} | |
| 173 ${library.paired_options.dovetail} | |
| 174 ${library.paired_options.no_contain} | |
| 175 ${library.paired_options.no_overlap} | |
| 176 #end if | |
| 0 | 177 #end if |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
178 |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
179 ## Read group information. |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
180 @define_read_group_helpers@ |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
181 #if str( $library.type ) == "single": |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
182 #set $rg_auto_name = $read_group_name_default($library.input_1) |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
183 #elif str( $library.type ) == "paired": |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
184 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
185 #else |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
186 #set $rg_auto_name = $read_group_name_default($library.input_1) |
| 2 | 187 #end if |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
188 @set_use_rg_var@ |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
189 @set_read_group_vars@ |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
190 #if $use_rg |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
191 $format_read_group("", $rg_id, '"', arg='--rg-id ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
192 $format_read_group("SM:", $rg_sm, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
193 $format_read_group("PL:", $rg_pl, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
194 $format_read_group("LB:", $rg_lb, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
195 $format_read_group("CN:", $rg_cn, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
196 $format_read_group("DS:", $rg_ds, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
197 $format_read_group("DT:", $rg_dt, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
198 $format_read_group("FO:", $rg_fo, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
199 $format_read_group("KS:", $rg_ks, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
200 $format_read_group("PG:", $rg_pg, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
201 $format_read_group("PI:", $rg_pi, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
202 $format_read_group("PU:", $rg_pu, '"', arg='--rg ') |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
203 #end if |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
204 |
| 2 | 205 ## Analysis type |
| 206 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ): | |
| 207 $analysis_type.presets | |
| 208 #elif str( $analysis_type.analysis_type_selector ) == "full": | |
| 209 #if str( $analysis_type.input_options.input_options_selector ) == "yes": | |
| 210 --skip "${analysis_type.input_options.skip}" | |
| 211 --qupto "${analysis_type.input_options.qupto}" | |
| 212 --trim5 "${analysis_type.input_options.trim5}" | |
| 213 --trim3 "${analysis_type.input_options.trim3}" | |
| 214 ${analysis_type.input_options.qv_encoding} | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
215 ${analysis_type.input_options.solexa_quals} |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
216 ${analysis_type.input_options.int_quals} |
| 0 | 217 #end if |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
218 |
| 2 | 219 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes": |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
220 -N "${analysis_type.alignment_options.N}" |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
221 -L "${analysis_type.alignment_options.L}" |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
222 -i "${analysis_type.alignment_options.i}" |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
223 --n-ceil "${analysis_type.alignment_options.n_ceil}" |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
224 --dpad "${analysis_type.alignment_options.dpad}" |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
225 --gbar "${analysis_type.alignment_options.gbar}" |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
226 ${analysis_type.alignment_options.ignore_quals} |
| 2 | 227 ${analysis_type.alignment_options.nofw} |
| 228 ${analysis_type.alignment_options.norc} | |
| 229 ${analysis_type.alignment_options.no_1mm_upfront} | |
| 230 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end": | |
| 231 --end-to-end | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
232 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}" |
| 2 | 233 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local": |
| 234 --local | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
235 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}" |
| 2 | 236 #end if |
| 237 #end if | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
238 |
| 2 | 239 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes": |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
240 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ): |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
241 --ma "${analysis_type.scoring_options.ma}" |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
242 #end if |
| 2 | 243 --mp "${analysis_type.scoring_options.mp}" |
| 244 --np "${analysis_type.scoring_options.np}" | |
| 245 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}" | |
| 246 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}" | |
| 247 #end if | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
248 |
| 2 | 249 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k": |
| 250 -k "${analysis_type.reporting_options.k}" | |
| 251 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a": | |
| 252 -a | |
| 253 #end if | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
254 |
| 2 | 255 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": |
| 256 -D "${analysis_type.effort_options.D}" | |
| 257 -R "${analysis_type.effort_options.R}" | |
| 258 #end if | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
259 |
| 2 | 260 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes": |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
261 ${analysis_type.sam_options.no_unal} |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
262 ${analysis_type.sam_options.omit_sec_seq} |
| 2 | 263 #end if |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
264 |
| 2 | 265 #if str( $analysis_type.other_options.other_options_selector ) == "yes": |
| 266 ${analysis_type.other_options.reorder} | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
267 ${analysis_type.other_options.non_deterministic} |
| 2 | 268 --seed "${analysis_type.other_options.seed}" |
| 0 | 269 #end if |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
270 |
| 2 | 271 #elif str( $analysis_type.analysis_type_selector ) == "cline": |
| 272 ${analysis_type.cline} | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
273 #end if |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
274 |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
275 ## mapping stats (i.e. stderr from bowtie2) |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
276 #if $save_mapping_stats |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
277 2> '$mapping_stats' |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
278 #end if |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
279 |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
280 ## output file |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
281 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ): |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
282 | samtools sort -O bam -o '$output' |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
283 #else |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
284 > '$output_sam' |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
285 #end if |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
286 |
| 0 | 287 ## rename unaligned sequence files |
| 288 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
289 #from os.path import splitext |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
290 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) ) |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
291 && mv "${ _unaligned_root }.1${_unaligned_ext}" '$output_unaligned_reads_l' |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
292 && mv "${ _unaligned_root }.2${_unaligned_ext}" '$output_unaligned_reads_r' |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
293 #end if |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
294 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r: |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
295 #from os.path import splitext |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
296 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) ) |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
297 && mv "${ _aligned_root }.1${_aligned_ext}" '$output_aligned_reads_l' |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
298 && mv "${ _aligned_root }.2${_aligned_ext}" '$output_aligned_reads_r' |
| 0 | 299 #end if |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
300 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
301 ]]></command> |
| 0 | 302 <inputs> |
| 303 <!-- single/paired --> | |
| 304 <conditional name="library"> | |
| 2 | 305 <param name="type" type="select" label="Is this single or paired library"> |
| 0 | 306 <option value="single">Single-end</option> |
| 307 <option value="paired">Paired-end</option> | |
| 2 | 308 <option value="paired_collection">Paired-end Dataset Collection</option> |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
309 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> |
| 0 | 310 </param> |
| 2 | 311 |
| 0 | 312 <when value="single"> |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
313 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file" help="Must be of datatype "fastqsanger"" /> |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
314 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
315 <expand macro="align_unalign" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
316 |
| 0 | 317 </when> |
| 318 <when value="paired"> | |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
319 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
320 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
321 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
322 <expand macro="align_unalign" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
323 <expand macro="paired_end_options" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
324 |
| 2 | 325 </when> |
| 326 <when value="paired_collection"> | |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
327 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger"" /> |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
328 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
329 <expand macro="align_unalign" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
330 <expand macro="paired_end_options" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
331 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
332 </when> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
333 <when value="paired_interleaved"> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
334 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger". --interleaved"/> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
335 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
336 <expand macro="align_unalign" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
337 <expand macro="paired_end_options" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
338 |
| 0 | 339 </when> |
| 340 </conditional> | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
341 |
| 0 | 342 <!-- reference genome --> |
| 343 <conditional name="reference_genome"> | |
| 2 | 344 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> |
| 345 <option value="indexed">Use a built-in genome index</option> | |
| 346 <option value="history">Use a genome from the history and build index</option> | |
| 0 | 347 </param> |
| 348 <when value="indexed"> | |
| 2 | 349 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
| 0 | 350 <options from_data_table="bowtie2_indexes"> |
| 351 <filter type="sort_by" column="2"/> | |
| 352 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 353 </options> | |
| 354 </param> | |
| 355 </when> | |
| 356 <when value="history"> | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
357 <param name="own_file" type="data" format="fasta" label="Select reference genome" /> |
| 0 | 358 </when> |
| 359 </conditional> | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
360 |
| 2 | 361 <!-- read group settings --> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
362 <expand macro="read_group_conditional" /> |
| 2 | 363 <conditional name="analysis_type"> |
| 364 <param name="analysis_type_selector" type="select" label="Select analysis mode"> | |
| 365 <option value="simple">1: Default setting only</option> | |
| 366 <option value="full">2: Full parameter list</option> | |
| 0 | 367 </param> |
| 2 | 368 <when value="simple"> |
| 369 <param name="presets" type="select" display="radio" label="Do you want to use presets?" help="Allow selecting among several preset parameter settings. Choosing between these will result in dramatic changes in runtime. See help below to understand effects of these presets."> | |
| 370 <option value="no_presets" selected="True">No, just use defaults</option> | |
| 371 <option value="--very-fast">Very fast end-to-end (--very-fast)</option> | |
| 372 <option value="--fast">Fast end-to-end (--fast)</option> | |
| 373 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option> | |
| 374 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option> | |
| 375 <option value="--very-fast-local">Very fast local (--very-fast-local)</option> | |
| 376 <option value="--fast-local">Fast local (--fast-local)</option> | |
| 377 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option> | |
| 378 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option> | |
| 0 | 379 </param> |
| 2 | 380 </when> |
| 381 <when value="full"> | |
| 382 <conditional name="input_options"> | |
| 383 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See "Input Options" section of Help below for information"> | |
| 384 <option value="yes">Yes</option> | |
| 385 <option value="no" selected="true">No</option> | |
| 386 </param> | |
| 387 <when value="yes"> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
388 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
389 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/> |
| 2 | 390 <param name="trim5" type="integer" min="0" value="0" label="Trim that many bases from 5' (left) end of each read before alignment" help="-5/--trim5; default=0"/> |
| 391 <param name="trim3" type="integer" min="0" value="0" label="Trim that many bases from 3' (right) end of each read before alignment" help="-3/--trim3; default=0"/> | |
| 392 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details"> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
393 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
394 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option> |
| 2 | 395 </param> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
396 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
397 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/> |
| 2 | 398 </when> |
| 399 <when value="no"> | |
| 400 <!-- do nothing --> | |
| 401 </when> | |
| 402 </conditional> | |
| 403 <conditional name="alignment_options"> | |
| 404 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See "Alignment Options" section of Help below for information"> | |
| 405 <option value="yes">Yes</option> | |
| 406 <option value="no" selected="true">No</option> | |
| 407 </param> | |
| 408 <when value="yes"> | |
| 409 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
410 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
411 <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
412 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
413 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/> |
| 2 | 414 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/> |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
415 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
416 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
417 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
418 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/> |
| 2 | 419 <conditional name="align_mode"> |
| 420 <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end"> | |
| 421 <option value="end-to-end" selected="True">End to End (--end-to-end)</option> | |
| 422 <option value="local">Local (--local)</option> | |
| 423 </param> | |
| 424 <when value="end-to-end"> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
425 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/> |
| 2 | 426 </when> |
| 427 <when value="local"> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
428 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/> |
| 2 | 429 </when> |
| 430 </conditional> | |
| 431 </when> | |
| 432 <when value="no"> | |
| 433 <!-- do nothing --> | |
| 434 </when> | |
| 435 </conditional> | |
| 436 <conditional name="scoring_options"> | |
| 437 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See "Scoring Options" section of Help below for information"> | |
| 438 <option value="yes">Yes</option> | |
| 439 <option value="no" selected="true">No</option> | |
| 440 </param> | |
| 441 <when value="yes"> | |
| 442 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma; In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
443 <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/> |
| 2 | 444 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/> |
| 445 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/> | |
| 446 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/> | |
| 447 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/> | |
| 448 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/> | |
| 449 </when> | |
| 450 <when value="no"> | |
| 451 <!-- do nothing --> | |
| 452 </when> | |
| 453 </conditional> | |
| 454 <conditional name="reporting_options"> | |
| 455 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See "Reporting Options" section of Help below for information on -k and -a options"> | |
| 456 <option value="no" selected="true">No, do not set</option> | |
| 457 <option value="k">Set -k option and enter -k value</option> | |
| 458 <option value="a">Set -a option</option> | |
| 459 </param> | |
| 460 <when value="no"> | |
| 461 <!-- do nothing --> | |
| 462 </when> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
463 <when value="k"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
464 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/> |
| 2 | 465 </when> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
466 <when value="a"> |
| 2 | 467 <!-- do nothing here; set -a flag on the command line--> |
| 468 </when> | |
| 469 </conditional> | |
| 470 <conditional name="effort_options"> | |
| 471 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See "Effort Options" section of Help below for information"> | |
| 472 <option value="yes">Yes</option> | |
| 473 <option value="no" selected="true">No</option> | |
| 474 </param> | |
| 475 <when value="yes"> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
476 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/> |
| 2 | 477 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/> |
| 478 </when> | |
| 479 <when value="no"> | |
| 480 <!-- do nothing --> | |
| 481 </when> | |
| 482 </conditional> | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
483 |
| 2 | 484 <conditional name="sam_options"> |
| 485 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See "Output Options" section of Help below for information"> | |
| 486 <option value="yes">Yes</option> | |
| 487 <option value="no" selected="true">No</option> | |
| 488 </param> | |
| 489 <when value="yes"> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
490 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
491 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/> |
| 2 | 492 </when> |
| 493 <when value="no"> | |
| 494 <!-- do nothing --> | |
| 495 </when> | |
| 496 </conditional> | |
| 497 <conditional name="other_options"> | |
| 498 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See "Other Options" section of Help below for information"> | |
| 499 <option value="yes">Yes</option> | |
| 500 <option value="no" selected="true">No</option> | |
| 501 </param> | |
| 502 <when value="yes"> | |
| 503 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file" help="--reorder; Default=False"/> | |
| 504 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
505 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/> |
| 2 | 506 </when> |
| 507 <when value="no"> | |
| 508 <!-- do nothing --> | |
| 509 </when> | |
| 510 </conditional> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
511 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/> |
| 0 | 512 </when> |
| 513 </conditional> | |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
514 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" /> |
| 0 | 515 </inputs> |
| 516 | |
| 517 <!-- define outputs --> | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
518 |
| 0 | 519 <outputs> |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
520 |
| 0 | 521 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > |
| 2 | 522 <filter>library['unaligned_file'] is True</filter> |
| 0 | 523 <actions> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
524 <conditional name="library.type"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
525 <when value="single"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
526 <action type="format"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
527 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
528 </action> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
529 </when> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
530 <when value="paired"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
531 <action type="format"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
532 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
533 </action> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
534 </when> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
535 <when value="paired_collection"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
536 <action type="format"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
537 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
538 </action> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
539 </when> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
540 </conditional> |
| 0 | 541 </actions> |
| 542 </data> | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
543 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" > |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
544 <filter>library['aligned_file'] is True</filter> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
545 <actions> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
546 <conditional name="library.type"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
547 <when value="single"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
548 <action type="format"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
549 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
550 </action> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
551 </when> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
552 <when value="paired"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
553 <action type="format"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
554 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
555 </action> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
556 </when> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
557 <when value="paired_collection"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
558 <action type="format"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
559 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
560 </action> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
561 </when> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
562 </conditional> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
563 </actions> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
564 </data> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
565 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
566 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
567 <actions> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
568 <conditional name="library.type"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
569 <when value="paired"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
570 <action type="format"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
571 <option type="from_param" name="library.input_2" param_attribute="ext" /> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
572 </action> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
573 </when> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
574 <when value="paired_collection"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
575 <action type="format"> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
576 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
577 </action> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
578 </when> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
579 </conditional> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
580 </actions> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
581 </data> |
| 0 | 582 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> |
| 2 | 583 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter> |
| 0 | 584 <actions> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
585 <conditional name="library.type"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
586 <when value="paired"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
587 <action type="format"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
588 <option type="from_param" name="library.input_2" param_attribute="ext" /> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
589 </action> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
590 </when> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
591 <when value="paired_collection"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
592 <action type="format"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
593 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
594 </action> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
595 </when> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
596 </conditional> |
| 0 | 597 </actions> |
| 598 </data> | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
599 |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
600 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
601 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter> |
| 0 | 602 <actions> |
| 603 <conditional name="reference_genome.source"> | |
| 604 <when value="indexed"> | |
| 605 <action type="metadata" name="dbkey"> | |
| 606 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> | |
| 607 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | |
| 608 <filter type="param_value" ref="reference_genome.index" column="0"/> | |
| 609 </option> | |
| 610 </action> | |
| 611 </when> | |
| 612 <when value="history"> | |
| 613 <action type="metadata" name="dbkey"> | |
| 614 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> | |
| 615 </action> | |
| 616 </when> | |
| 617 </conditional> | |
| 618 </actions> | |
| 619 </data> | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
620 |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
621 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
622 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
623 <actions> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
624 <conditional name="reference_genome.source"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
625 <when value="indexed"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
626 <action type="metadata" name="dbkey"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
627 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
628 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
629 <filter type="param_value" ref="reference_genome.index" column="0"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
630 </option> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
631 </action> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
632 </when> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
633 <when value="history"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
634 <action type="metadata" name="dbkey"> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
635 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
636 </action> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
637 </when> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
638 </conditional> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
639 </actions> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
640 </data> |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
641 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats"> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
642 <filter>save_mapping_stats is True</filter> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
643 </data> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
644 |
| 0 | 645 </outputs> |
| 646 | |
| 647 <tests> | |
| 648 <test> | |
| 649 <!-- basic test on single paired default run --> | |
| 2 | 650 <param name="type" value="paired"/> |
| 651 <param name="paired_options_selector" value="no"/> | |
| 0 | 652 <param name="unaligned_file" value="false"/> |
| 2 | 653 <param name="analysis_type_selector" value="simple"/> |
| 0 | 654 <param name="source" value="history" /> |
| 2 | 655 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
| 656 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> | |
| 657 <param name="own_file" value="bowtie2-ref.fasta" /> | |
| 658 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | |
| 0 | 659 </test> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
660 <test> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
661 <!-- basic test on single paired default run --> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
662 <param name="type" value="paired"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
663 <param name="paired_options_selector" value="no"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
664 <param name="unaligned_file" value="false"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
665 <param name="analysis_type_selector" value="simple"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
666 <param name="rg_selector" value="set"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
667 <param name="ID" value="rg1"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
668 <param name="PL" value="CAPILLARY"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
669 <param name="source" value="history" /> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
670 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
671 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
672 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
673 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
674 </test> |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
675 <test> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
676 <!-- basic test on single paired default run with stats--> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
677 <param name="type" value="paired"/> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
678 <param name="paired_options_selector" value="no"/> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
679 <param name="unaligned_file" value="false"/> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
680 <param name="analysis_type_selector" value="simple"/> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
681 <param name="source" value="history" /> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
682 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
683 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
684 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
685 <param name="save_mapping_stats" value="true" /> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
686 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
687 <output name="mapping_stats"> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
688 <assert_contents> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
689 <has_text text="of these" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
690 </assert_contents> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
691 </output> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
692 </test> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
693 <test> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
694 <!-- basic test on interleaved paired default run --> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
695 <param name="type" value="paired_interleaved"/> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
696 <!-- <param name="paired_options_selector" value="no"/> --> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
697 <param name="unaligned_file" value="false"/> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
698 <param name="analysis_type_selector" value="simple"/> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
699 <param name="rg_selector" value="set"/> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
700 <param name="ID" value="rg1"/> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
701 <param name="PL" value="CAPILLARY"/> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
702 <param name="source" value="history" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
703 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
704 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
705 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/> |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
706 </test> |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
707 <test> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
708 <!-- test fastqsanger.gz input --> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
709 <param name="type" value="paired"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
710 <param name="paired_options_selector" value="no"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
711 <param name="unaligned_file" value="false"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
712 <param name="analysis_type_selector" value="simple"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
713 <param name="source" value="history" /> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
714 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
715 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
716 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
717 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
718 </test> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
719 <test> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
720 <!-- test fastqsanger.bz2 input --> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
721 <param name="type" value="paired"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
722 <param name="paired_options_selector" value="no"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
723 <param name="unaligned_file" value="false"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
724 <param name="analysis_type_selector" value="simple"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
725 <param name="source" value="history" /> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
726 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
727 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
728 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
729 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> |
|
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
730 </test> |
| 0 | 731 </tests> |
| 732 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
733 <help><![CDATA[ |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
734 |
| 0 | 735 **Bowtie2 Overview** |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
736 |
| 2 | 737 Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site. |
| 738 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead. | |
| 739 | |
| 740 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/ | |
| 741 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml | |
| 742 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf | |
| 743 | |
| 744 ----- | |
| 0 | 745 |
| 2 | 746 **Selecting reference genomes for Bowtie2** |
| 747 | |
| 748 Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options: | |
| 0 | 749 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
750 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bowtie2-build utility and are ready to be mapped against. |
| 2 | 751 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using bowtie2-build command, and then run mapping with bowtie2. |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
752 |
| 2 | 753 If your genome of interest is not listed here you have two choices: |
| 754 | |
| 755 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added | |
| 756 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option. | |
| 0 | 757 |
| 758 ------ | |
| 759 | |
| 2 | 760 .. class:: infomark |
| 761 | |
| 762 **Bowtie2 options** | |
| 763 | |
| 764 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below. | |
| 765 | |
| 766 ----- | |
| 767 | |
| 0 | 768 **Inputs** |
| 769 | |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
770 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section). |
| 0 | 771 |
| 772 ------ | |
| 773 | |
| 2 | 774 **Input options**:: |
| 775 | |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
776 --interleaved |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
777 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair. |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
778 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
779 -s/--skip <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
780 Skip (i.e. do not align) the first `<int>` reads or pairs in the input. |
| 2 | 781 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
782 -u/--qupto <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
783 Align the first `<int>` reads or read pairs from the input (after the |
| 2 | 784 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit. |
| 785 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
786 -5/--trim5 <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
787 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0). |
| 0 | 788 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
789 -3/--trim3 <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
790 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0). |
| 2 | 791 |
| 792 --phred33 | |
| 793 Input qualities are ASCII chars equal to the Phred quality plus 33. This is | |
| 794 also called the "Phred+33" encoding, which is used by the very latest Illumina | |
| 795 pipelines. | |
| 796 | |
| 797 --phred64 | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
798 Input qualities are ASCII chars equal to the Phred quality plus 64. This is |
| 2 | 799 also called the "Phred+64" encoding. |
| 0 | 800 |
| 2 | 801 --solexa-quals |
| 802 Convert input qualities from Solexa Phred quality (which can be negative) to | |
| 803 Phred Phred quality (which can't). This scheme was used in older Illumina GA | |
| 804 Pipeline versions (prior to 1.3). Default: off. | |
| 805 | |
| 806 --int-quals | |
| 807 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`.... | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
808 Integers are treated as being on the Phred quality scale unless |
| 2 | 809 `--solexa-quals` is also specified. Default: off. |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
810 |
| 2 | 811 ------ |
| 812 | |
| 813 **Presets in `--end-to-end` mode**:: | |
| 814 | |
| 815 --very-fast | |
| 816 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50` | |
| 817 | |
| 818 --fast | |
| 819 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50` | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
820 |
| 2 | 821 --sensitive |
| 822 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode) | |
| 823 | |
| 824 --very-sensitive | |
| 825 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
| 0 | 826 |
| 827 ------ | |
| 828 | |
| 2 | 829 **Presets options in `--local` mode**:: |
| 0 | 830 |
| 2 | 831 --very-fast-local |
| 832 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00` | |
| 0 | 833 |
| 2 | 834 --fast-local |
| 835 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75` | |
| 0 | 836 |
| 2 | 837 --sensitive-local |
| 838 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode) | |
| 0 | 839 |
| 2 | 840 --very-sensitive-local |
| 841 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
842 |
| 0 | 843 ------ |
| 844 | |
| 2 | 845 **Alignment options**:: |
| 846 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
847 -N <int> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
848 Sets the number of mismatches to allowed in a seed alignment during multiseed |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
849 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower |
| 2 | 850 (often much slower) but increases sensitivity. Default: 0. |
| 851 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
852 -L <int> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
853 Sets the length of the seed substrings to align during multiseed alignment. |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
854 Smaller values make alignment slower but more sensitive. Default: the |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
855 `--sensitive` preset is used by default, which sets `-L` to 22 in |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
856 `--end-to-end` mode and to 20 in `--local` mode. |
| 2 | 857 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
858 -i <func> |
| 2 | 859 Sets a function governing the interval between seed substrings to use during |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
860 multiseed alignment. For instance, if the read has 30 characers, and seed |
| 2 | 861 length is 10, and the seed interval is 6, the seeds extracted will be: |
| 862 | |
| 863 Read: TAGCTACGCTCTACGCTATCATGCATAAAC | |
| 864 Seed 1 fw: TAGCTACGCT | |
| 865 Seed 1 rc: AGCGTAGCTA | |
| 866 Seed 2 fw: CGCTCTACGC | |
| 867 Seed 2 rc: GCGTAGAGCG | |
| 868 Seed 3 fw: ACGCTATCAT | |
| 869 Seed 3 rc: ATGATAGCGT | |
| 870 Seed 4 fw: TCATGCATAA | |
| 871 Seed 4 rc: TTATGCATGA | |
| 872 | |
| 873 Since it's best to use longer intervals for longer reads, this parameter sets | |
| 874 the interval as a function of the read length, rather than a single | |
| 875 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the | |
| 876 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
877 If the function returns a result less than |
| 2 | 878 1, it is rounded up to 1. Default: the `--sensitive` preset is used by |
| 879 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75` | |
| 880 in `--local` mode. | |
| 881 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
882 --n-ceil <func> |
| 2 | 883 Sets a function governing the maximum number of ambiguous characters (usually |
| 884 `N`s and/or `.`s) allowed in a read as a function of read length. For instance, | |
| 885 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
886 where x is the read length. Reads exceeding this ceiling are filtered out. |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
887 Default: `L,0,0.15`. |
| 2 | 888 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
889 --dpad <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
890 "Pads" dynamic programming problems by `<int>` columns on either side to allow |
| 2 | 891 gaps. Default: 15. |
| 892 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
893 --gbar <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
894 Disallow gaps within `<int>` positions of the beginning or end of the read. |
| 2 | 895 Default: 4. |
| 896 | |
| 897 --ignore-quals | |
| 898 When calculating a mismatch penalty, always consider the quality value at the | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
899 mismatched position to be the highest possible, regardless of the actual value. |
| 2 | 900 I.e. input is treated as though all quality values are high. This is also the |
| 901 default behavior when the input doesn't specify quality values (e.g. in `-f`, | |
| 902 `-r`, or `-c` modes). | |
| 0 | 903 |
| 2 | 904 --nofw/--norc |
| 905 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to | |
| 906 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will | |
| 907 not attempt to align unpaired reads against the reverse-complement (Crick) | |
| 908 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the | |
| 909 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those | |
| 910 paired-end configurations corresponding to fragments from the reverse-complement | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
911 (Crick) strand. Default: both strands enabled. |
| 2 | 912 |
| 913 --no-1mm-upfront | |
| 914 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
915 end-to-end alignment for the read *before* trying the multiseed heuristic. Such |
| 2 | 916 alignments can be found very quickly, and many short read alignments have exact or |
| 917 near-exact end-to-end alignments. However, this can lead to unexpected | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
918 alignments when the user also sets options governing the multiseed heuristic, |
| 2 | 919 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal |
| 920 to the length of the read, the user will be surprised to find 1-mismatch alignments | |
| 921 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
922 alignments before using the multiseed heuristic, which leads to the expected |
| 2 | 923 behavior when combined with options such as `-L` and `-N`. This comes at the |
| 924 expense of speed. | |
| 925 | |
| 926 --end-to-end | |
| 927 In this mode, Bowtie 2 requires that the entire read align from one end to the | |
| 928 other, without any trimming (or "soft clipping") of characters from either end. | |
| 929 The match bonus `--ma` always equals 0 in this mode, so all alignment scores | |
| 930 are less than or equal to 0, and the greatest possible alignment score is 0. | |
| 931 This is mutually exclusive with `--local`. `--end-to-end` is the default mode. | |
| 0 | 932 |
| 2 | 933 --local |
| 934 In this mode, Bowtie 2 does not require that the entire read align from one end | |
| 935 to the other. Rather, some characters may be omitted ("soft clipped") from the | |
| 936 ends in order to achieve the greatest possible alignment score. The match bonus | |
| 937 `--ma` is used in this mode, and the best possible alignment score is equal to | |
| 938 the match bonus (`--ma`) times the length of the read. Specifying `--local` | |
| 939 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying | |
| 940 the local version of the preset (`--very-fast-local`). This is mutually | |
| 941 exclusive with `--end-to-end`. `--end-to-end` is the default mode. | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
942 |
| 2 | 943 ----- |
| 944 | |
| 945 **Scoring options**:: | |
| 946 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
947 --ma <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
948 Sets the match bonus. In `--local` mode `<int>` is added to the alignment |
| 2 | 949 score for each position where a read character aligns to a reference character |
| 950 and the characters match. Not used in `--end-to-end` mode. Default: 2. | |
| 951 | |
| 952 --mp MX,MN | |
| 953 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A | |
| 954 number less than or equal to `MX` and greater than or equal to `MN` is | |
| 955 subtracted from the alignment score for each position where a read character | |
| 956 aligns to a reference character, the characters do not match, and neither is an | |
| 957 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. | |
| 958 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` | |
| 959 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2. | |
| 960 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
961 --np <int> |
| 2 | 962 Sets penalty for positions where the read, reference, or both, contain an |
| 963 ambiguous character such as `N`. Default: 1. | |
| 964 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
965 --rdg <int1>,<int2> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
966 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
967 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3. |
| 2 | 968 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
969 --rfg <int1>,<int2> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
970 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
971 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default: |
| 2 | 972 5, 3. |
| 0 | 973 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
974 --score-min <func> |
| 2 | 975 Sets a function governing the minimum alignment score needed for an alignment to |
| 976 be considered "valid" (i.e. good enough to report). This is a function of read | |
| 977 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
978 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and |
| 2 | 979 the default in `--local` mode is `G,20,8`. |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
980 |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
981 ----- |
| 2 | 982 |
| 983 **Reporting options**:: | |
| 984 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
985 -k <int> |
| 2 | 986 By default, `bowtie2` searches for distinct, valid alignments for each read. |
| 987 When it finds a valid alignment, it continues looking for alignments that are | |
| 988 nearly as good or better. The best alignment found is reported (randomly | |
| 989 selected from among best if tied). Information about the best alignments is | |
| 990 used to estimate mapping quality and to set SAM optional fields, such as | |
| 991 `AS:i` and `XS:i`. | |
| 992 | |
| 993 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
994 searches for at most `<int>` distinct, valid alignments for each read. The |
| 2 | 995 search terminates when it can't find more distinct valid alignments, or when it |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
996 finds `<int>`, whichever happens first. All alignments found are reported in |
| 2 | 997 descending order by alignment score. The alignment score for a paired-end |
| 998 alignment equals the sum of the alignment scores of the individual mates. Each | |
| 999 reported read or pair alignment beyond the first has the SAM 'secondary' bit | |
| 1000 (which equals 256) set in its FLAGS field. For reads that have more than | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1001 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1002 `<int>` alignments reported are the best possible in terms of alignment score. |
| 2 | 1003 `-k` is mutually exclusive with `-a`. |
| 0 | 1004 |
| 2 | 1005 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when |
| 1006 aligning reads to long, repetitive genomes large `-k` can be very, very slow. | |
| 1007 | |
| 1008 -a | |
| 1009 Like `-k` but with no upper limit on number of alignments to search for. `-a` | |
| 1010 is mutually exclusive with `-k`. | |
| 1011 | |
| 1012 Note: Bowtie 2 is not designed with `-a` mode in mind, and when | |
| 1013 aligning reads to long, repetitive genomes this mode can be very, very slow. | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1014 |
| 2 | 1015 ----- |
| 1016 | |
| 1017 **Effort options**:: | |
| 1018 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1019 -D <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1020 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2 |
| 2 | 1021 moves on, using the alignments found so far. A seed extension "fails" if it |
| 1022 does not yield a new best or a new second-best alignment. This limit is | |
| 1023 automatically adjusted up when -k or -a are specified. Default: 15. | |
| 1024 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1025 -R <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1026 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with |
| 2 | 1027 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads |
| 1028 (same length, same number of mismatches allowed) at different offsets and | |
| 1029 searches for more alignments. A read is considered to have repetitive seeds if | |
| 1030 the total number of seed hits divided by the number of seeds that aligned at | |
| 1031 least once is greater than 300. Default: 2. | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1032 |
| 2 | 1033 ----- |
| 1034 | |
| 1035 **Paired-end options**:: | |
| 0 | 1036 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1037 -I/--minins <int> |
| 2 | 1038 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is |
| 1039 specified and a paired-end alignment consists of two 20-bp alignments in the | |
| 1040 appropriate orientation with a 20-bp gap between them, that alignment is | |
| 1041 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not | |
| 1042 be valid in that case. If trimming options `-3` or `-5` are also used, the | |
| 1043 `-I` constraint is applied with respect to the untrimmed mates. | |
| 1044 | |
| 1045 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
| 1046 run. This is because larger differences bewteen `-I` and `-X` require that | |
| 1047 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
| 1048 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
| 1049 efficient. | |
| 1050 | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1051 Default: 0 (essentially imposing no minimum) |
| 2 | 1052 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1053 -X/--maxins <int> |
| 2 | 1054 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100` |
| 1055 is specified and a paired-end alignment consists of two 20-bp alignments in the | |
| 1056 proper orientation with a 60-bp gap between them, that alignment is considered | |
| 1057 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in | |
| 1058 that case. If trimming options `-3` or `-5` are also used, the `-X` | |
| 1059 constraint is applied with respect to the untrimmed mates, not the trimmed | |
| 1060 mates. | |
| 1061 | |
| 1062 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
| 1063 run. This is because larger differences bewteen `-I` and `-X` require that | |
| 1064 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
| 1065 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
| 1066 efficient. | |
| 1067 | |
| 1068 Default: 500. | |
| 0 | 1069 |
| 2 | 1070 --fr/--rf/--ff |
| 1071 The upstream/downstream mate orientations for a valid paired-end alignment | |
| 1072 against the forward reference strand. E.g., if `--fr` is specified and there is | |
| 1073 a candidate paired-end alignment where mate 1 appears upstream of the reverse | |
| 1074 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are | |
| 1075 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse | |
| 1076 complement of mate 1 and all other constraints are met, that too is valid. | |
| 1077 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a | |
| 1078 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1 | |
| 1079 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate | |
| 1080 for Illumina's Paired-end Sequencing Assay). | |
| 1081 | |
| 1082 --no-mixed | |
| 1083 By default, when `bowtie2` cannot find a concordant or discordant alignment for | |
| 1084 a pair, it then tries to find alignments for the individual mates. This option | |
| 1085 disables that behavior. | |
| 0 | 1086 |
| 2 | 1087 --no-discordant |
| 1088 By default, `bowtie2` looks for discordant alignments if it cannot find any | |
| 1089 concordant alignments. A discordant alignment is an alignment where both mates | |
| 1090 align uniquely, but that does not satisfy the paired-end constraints | |
| 1091 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior. | |
| 1092 | |
| 1093 --dovetail | |
| 1094 If the mates "dovetail", that is if one mate alignment extends past the | |
| 1095 beginning of the other such that the wrong mate begins upstream, consider that | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
1096 to be concordant. Default: mates cannot dovetail in a concordant alignment. |
| 2 | 1097 |
| 1098 --no-contain | |
| 1099 If one mate alignment contains the other, consider that to be non-concordant. | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
1100 Default: a mate can contain the other in a concordant alignment. |
| 2 | 1101 |
| 1102 --no-overlap | |
| 1103 If one mate alignment overlaps the other at all, consider that to be | |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
1104 non-concordant. Default: mates can overlap in a concordant alignment. |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1105 |
| 0 | 1106 ------ |
| 1107 | |
| 2 | 1108 **SAM options**:: |
| 0 | 1109 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1110 --rg-id <text> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1111 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1112 printed, with `<text>` as the value associated with the `ID:` tag. It also |
| 2 | 1113 causes the `RG:Z:` extra field to be attached to each SAM output record, with |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1114 value set to `<text>`. |
| 0 | 1115 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1116 --rg <text> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1117 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the |
| 2 | 1118 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id` |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
1119 must also be specified. This is because the `ID` tag is required by the SAM |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
1120 Specification. Specify `--rg` multiple times to set multiple fields. See the |
|
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
1121 SAM Specification for details about what fields are legal. |
| 0 | 1122 |
| 2 | 1123 --omit-sec-seq |
| 1124 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ` | |
| 1125 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix | |
| 1126 in those fields instead. | |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1127 |
| 2 | 1128 ----- |
| 0 | 1129 |
| 2 | 1130 **Other options**:: |
| 0 | 1131 |
| 2 | 1132 --reorder |
| 1133 Guarantees that output SAM records are printed in an order corresponding to the | |
| 1134 order of the reads in the original input file, even when `-p` is set greater | |
| 1135 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie | |
| 1136 2 to run somewhat slower and use somewhat more memory then if `--reorder` were | |
| 1137 not specified. Has no effect if `-p` is set to 1, since output order will | |
| 1138 naturally correspond to input order in that case. | |
| 0 | 1139 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1140 --seed <int> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1141 Use `<int>` as the seed for pseudo-random number generator. Default: 0. |
| 0 | 1142 |
| 2 | 1143 --non-deterministic |
| 1144 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It | |
| 1145 seeds the generator with a number derived from (a) the read name, (b) the | |
| 1146 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed` | |
| 1147 option. This means that if two reads are identical (same name, same | |
| 1148 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s) | |
| 1149 for both, even if there was ambiguity. When `--non-deterministic` is specified, | |
| 1150 Bowtie 2 re-initializes its pseudo-random generator for each read using the | |
| 1151 current time. This means that Bowtie 2 will not necessarily report the same | |
| 1152 alignment for two identical reads. This is counter-intuitive for some users, | |
| 1153 but might be more appropriate in situations where the input consists of many | |
| 1154 identical reads. | |
| 0 | 1155 |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1156 ----- |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1157 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1158 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1159 **Paired-end (and mate-pair) data in fastq format** |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1160 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1161 Paired end datasets can be represented as two individual datasets: |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1162 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1163 First dataset:: |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1164 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1165 @1/1 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1166 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1167 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1168 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1169 @2/1 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1170 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1171 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1172 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1173 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1174 Second dataset:: |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1175 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1176 @1/2 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1177 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1178 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1179 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1180 @2/2 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1181 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1182 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1183 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1184 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1185 Or a single *interleaved* dataset:: |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1186 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1187 @1/1 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1188 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1189 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1190 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1191 @1/2 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1192 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1193 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1194 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1195 @2/1 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1196 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1197 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1198 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1199 @2/2 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1200 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1201 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1202 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1203 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1204 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1205 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
1206 |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
1207 ]]></help> |
| 2 | 1208 <citations> |
| 1209 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> | |
| 1210 <citation type="doi">10.1038/nmeth.1923</citation> | |
| 1211 </citations> | |
| 0 | 1212 </tool> |