Mercurial > repos > devteam > bowtie2
annotate bowtie2_wrapper.xml @ 24:cd8b7d755af8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
author | iuc |
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date | Thu, 04 Apr 2019 09:39:19 -0400 |
parents | 5e52e98ff239 |
children | 739b008acace |
rev | line source |
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24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
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1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.3" profile="18.01"> |
2 | 2 <description>- map reads against reference genome</description> |
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
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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
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4 <import>bowtie2_macros.xml</import> |
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
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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
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6 <requirements> |
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
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7 <requirement type="package" version="2.3.4.1">bowtie2</requirement> |
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
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8 <requirement type="package" version="1.9">samtools</requirement> |
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
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diff
changeset
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9 </requirements> |
0 | 10 <version_command>bowtie2 --version</version_command> |
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fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
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changeset
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11 <command detect_errors="exit_code"><![CDATA[ |
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e798c0b3384c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents:
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diff
changeset
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12 ## Use pipefail if available to quit with first non-zero exit code |
e798c0b3384c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents:
20
diff
changeset
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13 set -o | grep -q pipefail && set -o pipefail; |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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14 ## prepare bowtie2 index |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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15 #set index_path = '' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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16 #if str($reference_genome.source) == "history": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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17 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome && |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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18 ln -s -f '$reference_genome.own_file' genome.fa && |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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19 #set index_path = 'genome' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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20 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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21 #set index_path = $reference_genome.index.fields.path |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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22 #end if |
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
23 |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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24 ## Link in the input files, so bowtie2 can tell their type |
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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25 |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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26 #set compressed="False" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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27 #set reads_are_fastq = True |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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28 #if str($library.type) == 'paired': |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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29 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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30 #set read1 = "input_f.fastq.gz" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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31 #set compressed = "GZ" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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32 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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33 #set read1 = "input_f.fastq.bz2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
34 #set compressed = "BZ2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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35 #else if $library.input_1.is_of_type('fasta'): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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36 #set reads_are_fastq = False |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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37 #set read1 = "input_f.fasta" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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38 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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39 #set read1 = "input_f.fastq" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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40 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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41 ln -f -s '${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
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42 |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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43 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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44 #set read2 = "input_r.fastq.gz" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
45 #set compressed = "GZ" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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46 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
47 #set read2 = "input_r.fastq.bz2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
48 #set compressed = "BZ2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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49 #else if $library.input_2.is_of_type('fasta'): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
50 #set read2 = "input_r.fasta" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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51 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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52 #set read2 = "input_r.fastq" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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53 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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54 ln -f -s '${library.input_2}' ${read2} && |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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55 #else if str($library.type) == 'paired_collection': |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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56 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
57 #set read1 = "input_f.fastq.gz" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
58 #set compressed = "GZ" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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59 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
60 #set read1 = "input_f.fastq.bz2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
61 #set compressed = "BZ2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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62 #else if $library.input_1.forward.is_of_type('fasta'): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
63 #set reads_are_fastq = False |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
64 #set read1 = "input_f.fasta" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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65 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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66 #set read1 = "input_f.fastq" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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67 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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68 ln -s '${library.input_1.forward}' ${read1} && |
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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69 |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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70 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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71 #set read2 = "input_r.fastq.gz" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
72 #set compressed = "GZ" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
73 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
74 #set read2 = "input_r.fastq.bz2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
75 #set compressed = "BZ2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
76 #else if $library.input_1.reverse.is_of_type("fasta"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
77 #set read2 = "input_r.fasta" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
78 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
79 #set read2 = "input_r.fastq" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
80 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
81 ln -s '${library.input_1.reverse}' ${read2} && |
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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diff
changeset
|
82 |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
83 #else if str($library.type) == 'paired_interleaved': |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
84 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
85 #set read1 = "input_il.fastq.gz" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
86 #set compressed = "GZ" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
87 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
88 #set read1 = "input_il.fastq.bz2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
89 #set compressed = "BZ2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
90 #else if $library.input_1.is_of_type("fasta"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
91 #set reads_are_fastq = False |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
92 #set read1 = "input_il.fasta" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
93 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
94 #set read1 = "input_il.fastq" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
95 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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96 ln -s '${library.input_1}' ${read1} && |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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97 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
99 #set read1 = "input_f.fastq.gz" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
|
100 #set compressed = "GZ" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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101 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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102 #set read1 = "input_f.fastq.bz2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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103 #set compressed = "BZ2" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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104 #else if $library.input_1.is_of_type("fasta"): |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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105 #set reads_are_fastq = False |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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106 #set read1 = "input_f.fasta" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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107 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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108 #set read1 = "input_f.fastq" |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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109 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff
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110 ln -s '${library.input_1}' ${read1} && |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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111 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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112 |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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113 ## execute bowtie2 |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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114 |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
115 bowtie2 |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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116 |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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117 ## number of threads |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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118 -p \${GALAXY_SLOTS:-4} |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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119 |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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120 ## index file path |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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121 -x '$index_path' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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122 |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
123 ## Input reads are fasta? |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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124 #if not reads_are_fastq: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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125 -f |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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126 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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127 |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff
changeset
|
128 ## Input reads |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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129 #if str( $library.type ) == "single": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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130 -U '${read1}' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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131 #if str( $library.unaligned_file ) == "true": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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132 #if $compressed == "GZ": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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133 --un-gz '${output_unaligned_reads_l}' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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134 #else if $compressed == "BZ2": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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|
135 --un-bz2 '${output_unaligned_reads_l}' |
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
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diff
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136 #else: |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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137 --un '${output_unaligned_reads_l}' |
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
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138 #end if |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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139 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff
changeset
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140 #if str( $library.aligned_file ) == "true": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
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141 #if $compressed == "GZ": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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142 --al-gz '${output_aligned_reads_l}' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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143 #else if $compressed == "BZ2": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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144 --al-bz2 '${output_aligned_reads_l}' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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145 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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146 --al '${output_aligned_reads_l}' |
16
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
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diff
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147 #end if |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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148 #end if |
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff
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149 |
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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150 #elif str( $library.type ) == "paired_interleaved": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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151 --interleaved '${read1}' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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152 #if str( $library.unaligned_file ) == "true": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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153 #if $compressed == "GZ": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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154 --un-gz '${output_unaligned_reads_l}' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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155 #else if $compressed == "BZ2": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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156 --un-bz2 '${output_unaligned_reads_l}' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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157 #else: |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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158 --un '${output_unaligned_reads_l}' |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
159 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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160 #end if |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
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161 #if str( $library.aligned_file ) == "true": |
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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162 #if $compressed == "GZ": |
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163 --al-gz '${output_aligned_reads_l}' |
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164 #else if $compressed == "BZ2": |
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165 --al-bz2 '${output_aligned_reads_l}' |
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166 #else: |
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167 --al '${output_aligned_reads_l}' |
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168 #end if |
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169 #end if |
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170 #else: |
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171 -1 '${read1}' |
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172 -2 '${read2}' |
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173 #if str( $library.unaligned_file ) == "true": |
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174 #if $compressed == "GZ": |
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175 --un-conc-gz '${output_unaligned_reads_l}' |
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176 #else if $compressed == "BZ2": |
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177 --un-conc-bz2 '${output_unaligned_reads_l}' |
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178 #else: |
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179 --un-conc '${output_unaligned_reads_l}' |
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180 #end if |
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181 #end if |
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182 #if str( $library.aligned_file ) == "true": |
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183 #if $compressed == "GZ": |
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184 --al-conc-gz '${output_aligned_reads_l}' |
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185 #else if $compressed == "BZ2": |
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186 --al-conc-bz2 '${output_aligned_reads_l}' |
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187 #else: |
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188 --al-conc '${output_aligned_reads_l}' |
0 | 189 #end if |
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190 #end if |
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191 #if str( $library.paired_options.paired_options_selector ) == "yes": |
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192 -I ${library.paired_options.I} |
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193 -X ${library.paired_options.X} |
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194 ${library.paired_options.fr_rf_ff} |
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195 ${library.paired_options.no_mixed} |
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196 ${library.paired_options.no_discordant} |
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197 ${library.paired_options.dovetail} |
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198 ${library.paired_options.no_contain} |
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199 ${library.paired_options.no_overlap} |
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200 #end if |
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201 #end if |
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202 |
18
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203 ## Read group information. |
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204 @define_read_group_helpers@ |
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205 #if str( $library.type ) == "single": |
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206 #set $rg_auto_name = $read_group_name_default($library.input_1) |
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207 #elif str( $library.type ) == "paired": |
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208 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) |
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209 #else |
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210 #set $rg_auto_name = $read_group_name_default($library.input_1) |
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211 #end if |
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212 @set_use_rg_var@ |
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213 @set_read_group_vars@ |
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214 #if $use_rg |
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215 $format_read_group("", $rg_id, '"', arg='--rg-id ') |
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216 $format_read_group("SM:", $rg_sm, '"', arg='--rg ') |
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217 $format_read_group("PL:", $rg_pl, '"', arg='--rg ') |
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218 $format_read_group("LB:", $rg_lb, '"', arg='--rg ') |
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219 $format_read_group("CN:", $rg_cn, '"', arg='--rg ') |
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220 $format_read_group("DS:", $rg_ds, '"', arg='--rg ') |
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221 $format_read_group("DT:", $rg_dt, '"', arg='--rg ') |
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222 $format_read_group("FO:", $rg_fo, '"', arg='--rg ') |
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223 $format_read_group("KS:", $rg_ks, '"', arg='--rg ') |
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224 $format_read_group("PG:", $rg_pg, '"', arg='--rg ') |
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225 $format_read_group("PI:", $rg_pi, '"', arg='--rg ') |
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226 $format_read_group("PU:", $rg_pu, '"', arg='--rg ') |
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227 #end if |
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228 |
18
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229 ## Analysis type |
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230 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ): |
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231 $analysis_type.presets |
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232 #elif str( $analysis_type.analysis_type_selector ) == "full": |
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233 #if str( $analysis_type.input_options.input_options_selector ) == "yes": |
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234 --skip ${analysis_type.input_options.skip} |
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235 --qupto ${analysis_type.input_options.qupto} |
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236 --trim5 ${analysis_type.input_options.trim5} |
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237 --trim3 ${analysis_type.input_options.trim3} |
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238 ${analysis_type.input_options.qv_encoding} |
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239 ${analysis_type.input_options.solexa_quals} |
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240 ${analysis_type.input_options.int_quals} |
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241 #end if |
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242 |
18
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243 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes": |
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244 -N ${analysis_type.alignment_options.N} |
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245 -L ${analysis_type.alignment_options.L} |
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246 -i '${analysis_type.alignment_options.i}' |
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247 --n-ceil '${analysis_type.alignment_options.n_ceil}' |
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248 --dpad ${analysis_type.alignment_options.dpad} |
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249 --gbar ${analysis_type.alignment_options.gbar} |
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250 ${analysis_type.alignment_options.ignore_quals} |
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251 ${analysis_type.alignment_options.nofw} |
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252 ${analysis_type.alignment_options.norc} |
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253 ${analysis_type.alignment_options.no_1mm_upfront} |
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254 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end": |
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255 --end-to-end |
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256 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}' |
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257 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local": |
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258 --local |
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259 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}' |
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260 #end if |
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261 #end if |
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262 |
18
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263 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes": |
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264 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ): |
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265 --ma ${analysis_type.scoring_options.ma} |
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266 #end if |
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267 --mp '${analysis_type.scoring_options.mp}' |
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268 --np ${analysis_type.scoring_options.np} |
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269 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend} |
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270 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend} |
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271 #end if |
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272 |
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273 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k": |
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274 -k ${analysis_type.reporting_options.k} |
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275 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a": |
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276 -a |
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277 #end if |
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278 |
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279 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": |
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280 -D ${analysis_type.effort_options.D} |
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281 -R ${analysis_type.effort_options.R} |
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282 #end if |
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283 #if str( $analysis_type.other_options.other_options_selector ) == "yes": |
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284 ${analysis_type.other_options.reorder} |
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285 ${analysis_type.other_options.non_deterministic} |
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286 --seed ${analysis_type.other_options.seed} |
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287 #end if |
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288 |
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289 #elif str( $analysis_type.analysis_type_selector ) == "cline": |
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290 ${analysis_type.cline} |
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291 #end if |
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292 |
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293 #if str( $sam_options.sam_options_selector ) == "yes": |
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294 ${sam_options.no_unal} |
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295 ${sam_options.omit_sec_seq} |
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296 ${sam_options.sam_no_qname_trunc} |
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297 ${sam_options.xeq} |
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298 ${sam_options.soft_clipped_unmapped_tlen} |
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299 ${sam_options.reorder} |
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300 #end if |
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301 |
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302 ## mapping stats (i.e. stderr from bowtie2) |
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303 #if $save_mapping_stats |
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304 2> '$mapping_stats' |
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305 #end if |
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306 |
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307 ## output file |
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308 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''): |
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309 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output' |
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310 #else if $sam_options.reorder: |
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311 | samtools view -bS - -o '$output' |
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312 #else: |
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313 > '$output' |
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314 #end if |
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315 |
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316 ## rename unaligned sequence files |
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317 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: |
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318 #from os.path import splitext |
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319 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) ) |
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320 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l' |
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321 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r' |
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322 #end if |
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323 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r: |
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324 #from os.path import splitext |
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325 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) ) |
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326 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l' |
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327 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r' |
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328 #end if |
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329 |
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330 ]]></command> |
0 | 331 <inputs> |
332 <!-- single/paired --> | |
333 <conditional name="library"> | |
2 | 334 <param name="type" type="select" label="Is this single or paired library"> |
0 | 335 <option value="single">Single-end</option> |
336 <option value="paired">Paired-end</option> | |
2 | 337 <option value="paired_collection">Paired-end Dataset Collection</option> |
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338 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> |
0 | 339 </param> |
2 | 340 |
0 | 341 <when value="single"> |
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342 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype "fastqsanger" or "fasta"" /> |
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343 <expand macro="align_unalign" /> |
0 | 344 </when> |
345 <when value="paired"> | |
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346 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype "fastqsanger"or "fasta"" /> |
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347 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype "fastqsanger"or "fasta"" /> |
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348 <expand macro="align_unalign" /> |
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349 <expand macro="paired_end_options" /> |
2 | 350 </when> |
351 <when value="paired_collection"> | |
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352 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" /> |
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353 <expand macro="align_unalign" /> |
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354 <expand macro="paired_end_options" /> |
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355 </when> |
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356 <when value="paired_interleaved"> |
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357 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/> |
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358 <expand macro="align_unalign" /> |
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359 <expand macro="paired_end_options" /> |
0 | 360 </when> |
361 </conditional> | |
362 <!-- reference genome --> | |
363 <conditional name="reference_genome"> | |
2 | 364 <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"> |
365 <option value="indexed">Use a built-in genome index</option> | |
366 <option value="history">Use a genome from the history and build index</option> | |
0 | 367 </param> |
368 <when value="indexed"> | |
2 | 369 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
0 | 370 <options from_data_table="bowtie2_indexes"> |
371 <filter type="sort_by" column="2"/> | |
372 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
373 </options> | |
374 </param> | |
375 </when> | |
376 <when value="history"> | |
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377 <param name="own_file" type="data" format="fasta" label="Select reference genome" /> |
0 | 378 </when> |
379 </conditional> | |
2 | 380 <!-- read group settings --> |
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381 <expand macro="read_group_conditional" /> |
2 | 382 <conditional name="analysis_type"> |
383 <param name="analysis_type_selector" type="select" label="Select analysis mode"> | |
384 <option value="simple">1: Default setting only</option> | |
385 <option value="full">2: Full parameter list</option> | |
0 | 386 </param> |
2 | 387 <when value="simple"> |
388 <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."> | |
389 <option value="no_presets" selected="True">No, just use defaults</option> | |
390 <option value="--very-fast">Very fast end-to-end (--very-fast)</option> | |
391 <option value="--fast">Fast end-to-end (--fast)</option> | |
392 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option> | |
393 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option> | |
394 <option value="--very-fast-local">Very fast local (--very-fast-local)</option> | |
395 <option value="--fast-local">Fast local (--fast-local)</option> | |
396 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option> | |
397 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option> | |
0 | 398 </param> |
2 | 399 </when> |
400 <when value="full"> | |
401 <conditional name="input_options"> | |
402 <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"> | |
403 <option value="yes">Yes</option> | |
404 <option value="no" selected="true">No</option> | |
405 </param> | |
406 <when value="yes"> | |
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407 <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"/> |
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408 <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 | 409 <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"/> |
410 <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"/> | |
411 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details"> | |
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412 <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> |
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413 <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 | 414 </param> |
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415 <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"/> |
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416 <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 | 417 </when> |
418 <when value="no"> | |
419 <!-- do nothing --> | |
420 </when> | |
421 </conditional> | |
422 <conditional name="alignment_options"> | |
423 <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"> | |
424 <option value="yes">Yes</option> | |
425 <option value="no" selected="true">No</option> | |
426 </param> | |
427 <when value="yes"> | |
428 <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"/> | |
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429 <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"/> |
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430 <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`"/> |
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431 <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`"/> |
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432 <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 | 433 <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"/> |
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434 <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"/> |
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435 <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"/> |
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436 <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"/> |
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437 <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 | 438 <conditional name="align_mode"> |
439 <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"> | |
440 <option value="end-to-end" selected="True">End to End (--end-to-end)</option> | |
441 <option value="local">Local (--local)</option> | |
442 </param> | |
443 <when value="end-to-end"> | |
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444 <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 | 445 </when> |
446 <when value="local"> | |
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447 <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 | 448 </when> |
449 </conditional> | |
450 </when> | |
451 <when value="no"> | |
452 <!-- do nothing --> | |
453 </when> | |
454 </conditional> | |
455 <conditional name="scoring_options"> | |
456 <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"> | |
457 <option value="yes">Yes</option> | |
458 <option value="no" selected="true">No</option> | |
459 </param> | |
460 <when value="yes"> | |
461 <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"/> | |
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462 <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 | 463 <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"/> |
464 <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"/> | |
465 <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"/> | |
466 <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"/> | |
467 <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"/> | |
468 </when> | |
469 <when value="no"> | |
470 <!-- do nothing --> | |
471 </when> | |
472 </conditional> | |
473 <conditional name="reporting_options"> | |
474 <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"> | |
475 <option value="no" selected="true">No, do not set</option> | |
476 <option value="k">Set -k option and enter -k value</option> | |
477 <option value="a">Set -a option</option> | |
478 </param> | |
479 <when value="no"> | |
480 <!-- do nothing --> | |
481 </when> | |
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482 <when value="k"> |
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483 <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 | 484 </when> |
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485 <when value="a"> |
2 | 486 <!-- do nothing here; set -a flag on the command line--> |
487 </when> | |
488 </conditional> | |
489 <conditional name="effort_options"> | |
490 <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"> | |
491 <option value="yes">Yes</option> | |
492 <option value="no" selected="true">No</option> | |
493 </param> | |
494 <when value="yes"> | |
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495 <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 | 496 <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"/> |
497 </when> | |
498 <when value="no"> | |
499 <!-- do nothing --> | |
500 </when> | |
501 </conditional> | |
502 <conditional name="other_options"> | |
503 <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"> | |
504 <option value="yes">Yes</option> | |
505 <option value="no" selected="true">No</option> | |
506 </param> | |
507 <when value="yes"> | |
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508 <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. If selected output file will not be coordinate sorted." help="--reorder; Default=False"/> |
2 | 509 <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"/> |
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510 <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 | 511 </when> |
512 <when value="no"> | |
513 <!-- do nothing --> | |
514 </when> | |
515 </conditional> | |
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516 </when> |
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517 </conditional> |
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518 <conditional name="sam_options"> |
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519 <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"> |
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520 <option value="yes">Yes</option> |
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521 <option value="no" selected="true">No</option> |
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522 </param> |
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523 <when value="yes"> |
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524 <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."/> |
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525 <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"/> |
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526 <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"/> |
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527 <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/> |
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528 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/> |
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529 <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/> |
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530 <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue="" |
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531 label="Reorder output to reflect order of the input file" |
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532 help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." /> |
0 | 533 </when> |
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534 <when value="no"/> |
0 | 535 </conditional> |
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536 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" /> |
0 | 537 </inputs> |
538 <!-- define outputs --> | |
539 <outputs> | |
540 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > | |
2 | 541 <filter>library['unaligned_file'] is True</filter> |
0 | 542 <actions> |
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543 <conditional name="library.type"> |
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544 <when value="single"> |
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545 <action type="format"> |
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546 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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547 </action> |
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548 </when> |
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549 <when value="paired"> |
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550 <action type="format"> |
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551 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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552 </action> |
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553 </when> |
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554 <when value="paired_collection"> |
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555 <action type="format"> |
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556 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
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557 </action> |
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558 </when> |
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559 </conditional> |
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560 <expand macro="dbKeyActions" /> |
0 | 561 </actions> |
562 </data> | |
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563 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" > |
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564 <filter>library['aligned_file'] is True</filter> |
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565 <actions> |
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566 <conditional name="library.type"> |
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567 <when value="single"> |
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568 <action type="format"> |
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569 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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570 </action> |
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571 </when> |
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572 <when value="paired"> |
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573 <action type="format"> |
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574 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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575 </action> |
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576 </when> |
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577 <when value="paired_collection"> |
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578 <action type="format"> |
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579 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
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580 </action> |
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581 </when> |
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582 </conditional> |
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583 <expand macro="dbKeyActions" /> |
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584 </actions> |
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585 </data> |
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586 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)"> |
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587 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter> |
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588 <actions> |
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589 <conditional name="library.type"> |
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590 <when value="paired"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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changeset
|
591 <action type="format"> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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changeset
|
592 <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
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|
593 </action> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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changeset
|
594 </when> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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changeset
|
595 <when value="paired_collection"> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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changeset
|
596 <action type="format"> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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changeset
|
597 <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
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changeset
|
598 </action> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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599 </when> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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600 </conditional> |
23
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changeset
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601 <expand macro="dbKeyActions" /> |
11
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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602 </actions> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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603 </data> |
0 | 604 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> |
2 | 605 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter> |
0 | 606 <actions> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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607 <conditional name="library.type"> |
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608 <when value="paired"> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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609 <action type="format"> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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610 <option type="from_param" name="library.input_2" param_attribute="ext" /> |
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611 </action> |
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612 </when> |
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613 <when value="paired_collection"> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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614 <action type="format"> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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|
615 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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|
616 </action> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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617 </when> |
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618 </conditional> |
23
5e52e98ff239
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changeset
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619 <expand macro="dbKeyActions" /> |
0 | 620 </actions> |
621 </data> | |
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
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622 <data format="bam" name="output" label="${tool.name} on ${on_string}: alignments"> |
22
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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623 <change_format> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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624 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" /> |
24
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
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625 <when input="sam_options.sam_opt" value="true" format="sam" /> |
22
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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|
626 </change_format> |
0 | 627 <actions> |
628 <conditional name="reference_genome.source"> | |
629 <when value="indexed"> | |
630 <action type="metadata" name="dbkey"> | |
631 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> | |
632 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | |
633 <filter type="param_value" ref="reference_genome.index" column="0"/> | |
634 </option> | |
635 </action> | |
636 </when> | |
637 <when value="history"> | |
638 <action type="metadata" name="dbkey"> | |
639 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> | |
640 </action> | |
641 </when> | |
642 </conditional> | |
23
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|
643 <expand macro="dbKeyActions" /> |
0 | 644 </actions> |
645 </data> | |
10
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|
646 <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
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647 <filter>save_mapping_stats is True</filter> |
23
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
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648 <actions> |
5e52e98ff239
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
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649 <expand macro="dbKeyActions" /> |
5e52e98ff239
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
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650 </actions> |
10
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|
651 </data> |
0 | 652 </outputs> |
653 <tests> | |
24
cd8b7d755af8
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654 <test expect_num_outputs="1"> |
17
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655 <!-- test on paired-end datasets --> |
2 | 656 <param name="type" value="paired"/> |
657 <param name="paired_options_selector" value="no"/> | |
0 | 658 <param name="unaligned_file" value="false"/> |
2 | 659 <param name="analysis_type_selector" value="simple"/> |
0 | 660 <param name="source" value="history" /> |
2 | 661 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
662 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> | |
663 <param name="own_file" value="bowtie2-ref.fasta" /> | |
664 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | |
0 | 665 </test> |
24
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666 <test expect_num_outputs="1"> |
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667 <!-- test on paired collection --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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668 <param name="type" value="paired_collection"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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669 <param name="paired_options_selector" value="no"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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670 <param name="unaligned_file" value="false"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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671 <param name="analysis_type_selector" value="simple"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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672 <param name="source" value="history" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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673 <param name="input_1"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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674 <collection type="paired"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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675 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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676 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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677 </collection> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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678 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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679 <param name="own_file" value="bowtie2-ref.fasta" /> |
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680 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> |
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681 </test> |
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682 <test expect_num_outputs="1"> |
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683 <!-- test on paired-end datasets with read group info --> |
5
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684 <param name="type" value="paired"/> |
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685 <param name="paired_options_selector" value="no"/> |
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686 <param name="unaligned_file" value="false"/> |
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687 <param name="analysis_type_selector" value="simple"/> |
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688 <param name="rg_selector" value="set"/> |
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689 <param name="ID" value="rg1"/> |
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690 <param name="PL" value="CAPILLARY"/> |
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691 <param name="source" value="history" /> |
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692 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
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693 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
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694 <param name="own_file" value="bowtie2-ref.fasta" /> |
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695 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> |
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696 </test> |
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697 <test expect_num_outputs="2"> |
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698 <!-- test on paired-end datasets with stats output --> |
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699 <param name="type" value="paired"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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700 <param name="paired_options_selector" value="no"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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701 <param name="unaligned_file" value="false"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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702 <param name="analysis_type_selector" value="simple"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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703 <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
|
704 <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
|
705 <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
|
706 <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
|
707 <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
|
708 <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
|
709 <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
|
710 <assert_contents> |
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
711 <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
|
712 </assert_contents> |
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
713 </output> |
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
714 </test> |
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
715 <test expect_num_outputs="1"> |
17
69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents:
16
diff
changeset
|
716 <!-- test on interleaved dataset --> |
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
14
diff
changeset
|
717 <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
|
718 <!-- <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
|
719 <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
|
720 <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
|
721 <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
|
722 <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
|
723 <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
|
724 <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
|
725 <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
|
726 <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
|
727 <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
|
728 </test> |
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
729 <test expect_num_outputs="1"> |
17
69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents:
16
diff
changeset
|
730 <!-- test on fastqsanger.gz paired-end datasets --> |
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
731 <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
|
732 <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
|
733 <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
|
734 <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
|
735 <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
|
736 <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
|
737 <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
|
738 <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
|
739 <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
|
740 </test> |
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
741 <test expect_num_outputs="1"> |
17
69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents:
16
diff
changeset
|
742 <!-- test on fastqsanger.bz2 paired-end datasets --> |
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
743 <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
|
744 <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
|
745 <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
|
746 <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
|
747 <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
|
748 <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
|
749 <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
|
750 <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
|
751 <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
|
752 </test> |
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
753 <test expect_num_outputs="1"> |
17
69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents:
16
diff
changeset
|
754 <!-- test on fasta paired-end datasets --> |
16
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
755 <param name="type" value="paired"/> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
756 <param name="paired_options_selector" value="no"/> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
757 <param name="unaligned_file" value="false"/> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
758 <param name="analysis_type_selector" value="simple"/> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
759 <param name="source" value="history" /> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
760 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
761 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
762 <param name="own_file" value="bowtie2-ref.fasta" /> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
763 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/> |
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
764 </test> |
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
765 <test expect_num_outputs="1"> |
22
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
766 <!-- test on fasta paired-end datasets with bam_native as output --> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
767 <param name="type" value="paired"/> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
768 <param name="paired_options_selector" value="no"/> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
769 <param name="unaligned_file" value="false"/> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
770 <param name="analysis_type_selector" value="simple"/> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
771 <param name="source" value="history" /> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
772 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
773 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
774 <param name="own_file" value="bowtie2-ref.fasta" /> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
775 <param name="sam_options_selector" value="yes" /> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
776 <param name="reorder" value="true" /> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
777 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/> |
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
778 </test> |
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
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779 <test expect_num_outputs="1"> |
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780 <!-- test on fasta paired-end datasets with sam as output --> |
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781 <param name="type" value="paired"/> |
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782 <param name="paired_options_selector" value="no"/> |
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783 <param name="unaligned_file" value="false"/> |
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784 <param name="analysis_type_selector" value="simple"/> |
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785 <param name="source" value="history" /> |
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786 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> |
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787 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> |
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788 <param name="own_file" value="bowtie2-ref.fasta" /> |
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789 <param name="sam_options_selector" value="yes" /> |
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790 <param name="sam_options|sam_opt" value="true" /> |
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791 <output name="output" ftype="sam"> |
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792 <assert_contents> |
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793 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" /> |
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794 </assert_contents> |
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795 </output> |
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796 </test> |
0 | 797 </tests> |
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798 <help><![CDATA[ |
0 | 799 **Bowtie2 Overview** |
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800 |
2 | 801 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. |
802 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead. | |
803 | |
804 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/ | |
805 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml | |
806 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf | |
807 | |
808 ----- | |
0 | 809 |
2 | 810 **Selecting reference genomes for Bowtie2** |
811 | |
812 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 | 813 |
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814 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 | 815 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. |
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816 |
2 | 817 If your genome of interest is not listed here you have two choices: |
818 | |
819 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 | |
820 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 | 821 |
822 ------ | |
823 | |
2 | 824 .. class:: infomark |
825 | |
826 **Bowtie2 options** | |
827 | |
828 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below. | |
829 | |
830 ----- | |
831 | |
0 | 832 **Inputs** |
833 | |
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834 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 | 835 |
836 ------ | |
837 | |
2 | 838 **Input options**:: |
839 | |
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840 --interleaved |
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841 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair. |
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842 |
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843 -s/--skip <int> |
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844 Skip (i.e. do not align) the first `<int>` reads or pairs in the input. |
2 | 845 |
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846 -u/--qupto <int> |
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847 Align the first `<int>` reads or read pairs from the input (after the |
2 | 848 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit. |
849 | |
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850 -5/--trim5 <int> |
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851 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0). |
0 | 852 |
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853 -3/--trim3 <int> |
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854 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0). |
2 | 855 |
856 --phred33 | |
857 Input qualities are ASCII chars equal to the Phred quality plus 33. This is | |
858 also called the "Phred+33" encoding, which is used by the very latest Illumina | |
859 pipelines. | |
860 | |
861 --phred64 | |
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862 Input qualities are ASCII chars equal to the Phred quality plus 64. This is |
2 | 863 also called the "Phred+64" encoding. |
0 | 864 |
2 | 865 --solexa-quals |
866 Convert input qualities from Solexa Phred quality (which can be negative) to | |
867 Phred Phred quality (which can't). This scheme was used in older Illumina GA | |
868 Pipeline versions (prior to 1.3). Default: off. | |
869 | |
870 --int-quals | |
871 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`.... | |
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872 Integers are treated as being on the Phred quality scale unless |
2 | 873 `--solexa-quals` is also specified. Default: off. |
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874 |
2 | 875 ------ |
876 | |
877 **Presets in `--end-to-end` mode**:: | |
878 | |
879 --very-fast | |
880 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50` | |
881 | |
882 --fast | |
883 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50` | |
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884 |
2 | 885 --sensitive |
886 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode) | |
887 | |
888 --very-sensitive | |
889 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
0 | 890 |
891 ------ | |
892 | |
2 | 893 **Presets options in `--local` mode**:: |
0 | 894 |
2 | 895 --very-fast-local |
896 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00` | |
0 | 897 |
2 | 898 --fast-local |
899 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75` | |
0 | 900 |
2 | 901 --sensitive-local |
902 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode) | |
0 | 903 |
2 | 904 --very-sensitive-local |
905 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
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906 |
0 | 907 ------ |
908 | |
2 | 909 **Alignment options**:: |
910 | |
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911 -N <int> |
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912 Sets the number of mismatches to allowed in a seed alignment during multiseed |
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913 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower |
2 | 914 (often much slower) but increases sensitivity. Default: 0. |
915 | |
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916 -L <int> |
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917 Sets the length of the seed substrings to align during multiseed alignment. |
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918 Smaller values make alignment slower but more sensitive. Default: the |
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919 `--sensitive` preset is used by default, which sets `-L` to 22 in |
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920 `--end-to-end` mode and to 20 in `--local` mode. |
2 | 921 |
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922 -i <func> |
2 | 923 Sets a function governing the interval between seed substrings to use during |
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924 multiseed alignment. For instance, if the read has 30 characers, and seed |
2 | 925 length is 10, and the seed interval is 6, the seeds extracted will be: |
926 | |
927 Read: TAGCTACGCTCTACGCTATCATGCATAAAC | |
928 Seed 1 fw: TAGCTACGCT | |
929 Seed 1 rc: AGCGTAGCTA | |
930 Seed 2 fw: CGCTCTACGC | |
931 Seed 2 rc: GCGTAGAGCG | |
932 Seed 3 fw: ACGCTATCAT | |
933 Seed 3 rc: ATGATAGCGT | |
934 Seed 4 fw: TCATGCATAA | |
935 Seed 4 rc: TTATGCATGA | |
936 | |
937 Since it's best to use longer intervals for longer reads, this parameter sets | |
938 the interval as a function of the read length, rather than a single | |
939 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the | |
940 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. | |
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941 If the function returns a result less than |
2 | 942 1, it is rounded up to 1. Default: the `--sensitive` preset is used by |
943 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75` | |
944 in `--local` mode. | |
945 | |
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946 --n-ceil <func> |
2 | 947 Sets a function governing the maximum number of ambiguous characters (usually |
948 `N`s and/or `.`s) allowed in a read as a function of read length. For instance, | |
949 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, | |
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950 where x is the read length. Reads exceeding this ceiling are filtered out. |
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951 Default: `L,0,0.15`. |
2 | 952 |
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953 --dpad <int> |
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954 "Pads" dynamic programming problems by `<int>` columns on either side to allow |
2 | 955 gaps. Default: 15. |
956 | |
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957 --gbar <int> |
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958 Disallow gaps within `<int>` positions of the beginning or end of the read. |
2 | 959 Default: 4. |
960 | |
961 --ignore-quals | |
962 When calculating a mismatch penalty, always consider the quality value at the | |
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963 mismatched position to be the highest possible, regardless of the actual value. |
2 | 964 I.e. input is treated as though all quality values are high. This is also the |
965 default behavior when the input doesn't specify quality values (e.g. in `-f`, | |
966 `-r`, or `-c` modes). | |
0 | 967 |
2 | 968 --nofw/--norc |
969 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to | |
970 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will | |
971 not attempt to align unpaired reads against the reverse-complement (Crick) | |
972 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the | |
973 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those | |
974 paired-end configurations corresponding to fragments from the reverse-complement | |
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975 (Crick) strand. Default: both strands enabled. |
2 | 976 |
977 --no-1mm-upfront | |
978 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch | |
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979 end-to-end alignment for the read *before* trying the multiseed heuristic. Such |
2 | 980 alignments can be found very quickly, and many short read alignments have exact or |
981 near-exact end-to-end alignments. However, this can lead to unexpected | |
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982 alignments when the user also sets options governing the multiseed heuristic, |
2 | 983 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal |
984 to the length of the read, the user will be surprised to find 1-mismatch alignments | |
985 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end | |
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986 alignments before using the multiseed heuristic, which leads to the expected |
2 | 987 behavior when combined with options such as `-L` and `-N`. This comes at the |
988 expense of speed. | |
989 | |
990 --end-to-end | |
991 In this mode, Bowtie 2 requires that the entire read align from one end to the | |
992 other, without any trimming (or "soft clipping") of characters from either end. | |
993 The match bonus `--ma` always equals 0 in this mode, so all alignment scores | |
994 are less than or equal to 0, and the greatest possible alignment score is 0. | |
995 This is mutually exclusive with `--local`. `--end-to-end` is the default mode. | |
0 | 996 |
2 | 997 --local |
998 In this mode, Bowtie 2 does not require that the entire read align from one end | |
999 to the other. Rather, some characters may be omitted ("soft clipped") from the | |
1000 ends in order to achieve the greatest possible alignment score. The match bonus | |
1001 `--ma` is used in this mode, and the best possible alignment score is equal to | |
1002 the match bonus (`--ma`) times the length of the read. Specifying `--local` | |
1003 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying | |
1004 the local version of the preset (`--very-fast-local`). This is mutually | |
1005 exclusive with `--end-to-end`. `--end-to-end` is the default mode. | |
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1006 |
2 | 1007 ----- |
1008 | |
1009 **Scoring options**:: | |
1010 | |
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1011 --ma <int> |
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1012 Sets the match bonus. In `--local` mode `<int>` is added to the alignment |
2 | 1013 score for each position where a read character aligns to a reference character |
1014 and the characters match. Not used in `--end-to-end` mode. Default: 2. | |
1015 | |
1016 --mp MX,MN | |
1017 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A | |
1018 number less than or equal to `MX` and greater than or equal to `MN` is | |
1019 subtracted from the alignment score for each position where a read character | |
1020 aligns to a reference character, the characters do not match, and neither is an | |
1021 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. | |
1022 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` | |
1023 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2. | |
1024 | |
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1025 --np <int> |
2 | 1026 Sets penalty for positions where the read, reference, or both, contain an |
1027 ambiguous character such as `N`. Default: 1. | |
1028 | |
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1029 --rdg <int1>,<int2> |
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1030 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of |
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1031 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3. |
2 | 1032 |
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1033 --rfg <int1>,<int2> |
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1034 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A |
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1035 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default: |
2 | 1036 5, 3. |
0 | 1037 |
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1038 --score-min <func> |
2 | 1039 Sets a function governing the minimum alignment score needed for an alignment to |
1040 be considered "valid" (i.e. good enough to report). This is a function of read | |
1041 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` | |
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1042 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 | 1043 the default in `--local` mode is `G,20,8`. |
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1044 |
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1045 ----- |
2 | 1046 |
1047 **Reporting options**:: | |
1048 | |
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1049 -k <int> |
2 | 1050 By default, `bowtie2` searches for distinct, valid alignments for each read. |
1051 When it finds a valid alignment, it continues looking for alignments that are | |
1052 nearly as good or better. The best alignment found is reported (randomly | |
1053 selected from among best if tied). Information about the best alignments is | |
1054 used to estimate mapping quality and to set SAM optional fields, such as | |
1055 `AS:i` and `XS:i`. | |
1056 | |
1057 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it | |
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1058 searches for at most `<int>` distinct, valid alignments for each read. The |
2 | 1059 search terminates when it can't find more distinct valid alignments, or when it |
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1060 finds `<int>`, whichever happens first. All alignments found are reported in |
2 | 1061 descending order by alignment score. The alignment score for a paired-end |
1062 alignment equals the sum of the alignment scores of the individual mates. Each | |
1063 reported read or pair alignment beyond the first has the SAM 'secondary' bit | |
1064 (which equals 256) set in its FLAGS field. For reads that have more than | |
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1065 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the |
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1066 `<int>` alignments reported are the best possible in terms of alignment score. |
2 | 1067 `-k` is mutually exclusive with `-a`. |
0 | 1068 |
2 | 1069 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when |
1070 aligning reads to long, repetitive genomes large `-k` can be very, very slow. | |
1071 | |
1072 -a | |
1073 Like `-k` but with no upper limit on number of alignments to search for. `-a` | |
1074 is mutually exclusive with `-k`. | |
1075 | |
1076 Note: Bowtie 2 is not designed with `-a` mode in mind, and when | |
1077 aligning reads to long, repetitive genomes this mode can be very, very slow. | |
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1078 |
2 | 1079 ----- |
1080 | |
1081 **Effort options**:: | |
1082 | |
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1083 -D <int> |
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1084 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2 |
2 | 1085 moves on, using the alignments found so far. A seed extension "fails" if it |
1086 does not yield a new best or a new second-best alignment. This limit is | |
1087 automatically adjusted up when -k or -a are specified. Default: 15. | |
1088 | |
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1089 -R <int> |
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1090 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with |
2 | 1091 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads |
1092 (same length, same number of mismatches allowed) at different offsets and | |
1093 searches for more alignments. A read is considered to have repetitive seeds if | |
1094 the total number of seed hits divided by the number of seeds that aligned at | |
1095 least once is greater than 300. Default: 2. | |
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1096 |
2 | 1097 ----- |
1098 | |
1099 **Paired-end options**:: | |
0 | 1100 |
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1101 -I/--minins <int> |
2 | 1102 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is |
1103 specified and a paired-end alignment consists of two 20-bp alignments in the | |
1104 appropriate orientation with a 20-bp gap between them, that alignment is | |
1105 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not | |
1106 be valid in that case. If trimming options `-3` or `-5` are also used, the | |
1107 `-I` constraint is applied with respect to the untrimmed mates. | |
1108 | |
1109 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
1110 run. This is because larger differences bewteen `-I` and `-X` require that | |
1111 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
1112 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
1113 efficient. | |
1114 | |
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1115 Default: 0 (essentially imposing no minimum) |
2 | 1116 |
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1117 -X/--maxins <int> |
2 | 1118 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100` |
1119 is specified and a paired-end alignment consists of two 20-bp alignments in the | |
1120 proper orientation with a 60-bp gap between them, that alignment is considered | |
1121 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in | |
1122 that case. If trimming options `-3` or `-5` are also used, the `-X` | |
1123 constraint is applied with respect to the untrimmed mates, not the trimmed | |
1124 mates. | |
1125 | |
1126 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
1127 run. This is because larger differences bewteen `-I` and `-X` require that | |
1128 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
1129 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
1130 efficient. | |
1131 | |
1132 Default: 500. | |
0 | 1133 |
2 | 1134 --fr/--rf/--ff |
1135 The upstream/downstream mate orientations for a valid paired-end alignment | |
1136 against the forward reference strand. E.g., if `--fr` is specified and there is | |
1137 a candidate paired-end alignment where mate 1 appears upstream of the reverse | |
1138 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are | |
1139 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse | |
1140 complement of mate 1 and all other constraints are met, that too is valid. | |
1141 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a | |
1142 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1 | |
1143 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate | |
1144 for Illumina's Paired-end Sequencing Assay). | |
1145 | |
1146 --no-mixed | |
1147 By default, when `bowtie2` cannot find a concordant or discordant alignment for | |
1148 a pair, it then tries to find alignments for the individual mates. This option | |
1149 disables that behavior. | |
0 | 1150 |
2 | 1151 --no-discordant |
1152 By default, `bowtie2` looks for discordant alignments if it cannot find any | |
1153 concordant alignments. A discordant alignment is an alignment where both mates | |
1154 align uniquely, but that does not satisfy the paired-end constraints | |
1155 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior. | |
1156 | |
1157 --dovetail | |
1158 If the mates "dovetail", that is if one mate alignment extends past the | |
1159 beginning of the other such that the wrong mate begins upstream, consider that | |
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1160 to be concordant. Default: mates cannot dovetail in a concordant alignment. |
2 | 1161 |
1162 --no-contain | |
1163 If one mate alignment contains the other, consider that to be non-concordant. | |
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1164 Default: a mate can contain the other in a concordant alignment. |
2 | 1165 |
1166 --no-overlap | |
1167 If one mate alignment overlaps the other at all, consider that to be | |
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1168 non-concordant. Default: mates can overlap in a concordant alignment. |
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1169 |
0 | 1170 ------ |
1171 | |
2 | 1172 **SAM options**:: |
0 | 1173 |
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1174 --rg-id <text> |
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1175 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be |
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1176 printed, with `<text>` as the value associated with the `ID:` tag. It also |
2 | 1177 causes the `RG:Z:` extra field to be attached to each SAM output record, with |
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1178 value set to `<text>`. |
0 | 1179 |
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1180 --rg <text> |
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1181 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the |
2 | 1182 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id` |
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1183 must also be specified. This is because the `ID` tag is required by the SAM |
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1184 Specification. Specify `--rg` multiple times to set multiple fields. See the |
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1185 SAM Specification for details about what fields are legal. |
0 | 1186 |
2 | 1187 --omit-sec-seq |
1188 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ` | |
1189 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix | |
1190 in those fields instead. | |
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1191 |
2 | 1192 ----- |
0 | 1193 |
2 | 1194 **Other options**:: |
0 | 1195 |
2 | 1196 --reorder |
1197 Guarantees that output SAM records are printed in an order corresponding to the | |
1198 order of the reads in the original input file, even when `-p` is set greater | |
1199 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie | |
1200 2 to run somewhat slower and use somewhat more memory then if `--reorder` were | |
1201 not specified. Has no effect if `-p` is set to 1, since output order will | |
1202 naturally correspond to input order in that case. | |
0 | 1203 |
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1204 --seed <int> |
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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1205 Use `<int>` as the seed for pseudo-random number generator. Default: 0. |
0 | 1206 |
2 | 1207 --non-deterministic |
1208 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It | |
1209 seeds the generator with a number derived from (a) the read name, (b) the | |
1210 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed` | |
1211 option. This means that if two reads are identical (same name, same | |
1212 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s) | |
1213 for both, even if there was ambiguity. When `--non-deterministic` is specified, | |
1214 Bowtie 2 re-initializes its pseudo-random generator for each read using the | |
1215 current time. This means that Bowtie 2 will not necessarily report the same | |
1216 alignment for two identical reads. This is counter-intuitive for some users, | |
1217 but might be more appropriate in situations where the input consists of many | |
1218 identical reads. | |
0 | 1219 |
15
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1220 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1221 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1222 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1223 **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
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1224 |
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1225 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
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1226 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1227 First dataset:: |
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1228 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1229 @1/1 |
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1230 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1231 + |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1232 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1233 @2/1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1234 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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1235 + |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1236 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG |
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1237 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1238 Second dataset:: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1239 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1240 @1/2 |
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1241 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1242 + |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1243 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1244 @2/2 |
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1245 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1246 + |
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1247 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH |
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1248 |
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1249 Or a single *interleaved* dataset:: |
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1250 |
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1251 @1/1 |
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1252 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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1253 + |
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1254 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1255 @1/2 |
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1256 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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1257 + |
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1258 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1259 @2/1 |
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1260 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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1261 + |
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1262 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG |
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1263 @2/2 |
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1264 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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1265 + |
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1266 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH |
11
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1267 ]]></help> |
2 | 1268 <citations> |
17
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1269 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> |
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1270 <citation type="doi">10.1038/nmeth.1923</citation> |
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1271 </citations> |
0 | 1272 </tool> |