Mercurial > repos > devteam > bowtie2
annotate bowtie2_wrapper.xml @ 14:937aa69e715f draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
| author | devteam |
|---|---|
| date | Wed, 12 Apr 2017 17:09:42 -0400 |
| parents | 12450efac659 |
| children | 43d12513224b |
| rev | line source |
|---|---|
|
14
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
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changeset
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1 <tool id="bowtie2" name="Bowtie2" version="2.3.0.1" profile="17.01"> |
| 2 | 2 <description>- map reads against reference genome</description> |
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42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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changeset
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3 <macros> |
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42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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changeset
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4 <import>read_group_macros.xml</import> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
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changeset
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5 </macros> |
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11
b4e9cf5f2ae8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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parents:
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changeset
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6 <requirements> |
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781e3a3b9d31
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a326a3469adfd33babe792cf58544438582a56a1
devteam
parents:
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diff
changeset
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7 <requirement type="package" version="2.3.0">bowtie2</requirement> |
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11
b4e9cf5f2ae8
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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8 <requirement type="package" version="1.3.1">samtools</requirement> |
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b4e9cf5f2ae8
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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11
b4e9cf5f2ae8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
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changeset
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11 <command detect_errors="exit_code"><![CDATA[ |
| 0 | 12 ## prepare bowtie2 index |
| 13 #set index_path = '' | |
| 14 #if str($reference_genome.source) == "history": | |
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11
b4e9cf5f2ae8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
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15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome && |
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b4e9cf5f2ae8
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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16 ln -s -f '$reference_genome.own_file' genome.fa && |
| 0 | 17 #set index_path = 'genome' |
| 18 #else: | |
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13
12450efac659
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit b22fc2e7243522b264f3d5d00706df8d18366405
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parents:
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changeset
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19 #set index_path = $reference_genome.index.fields.path |
| 0 | 20 #end if |
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7
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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diff
changeset
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21 |
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14
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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22 ## Link in the input files, so bowtie2 can tell their type |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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23 |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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24 #set compressed="False" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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25 #if str($library.type) == 'paired': |
|
937aa69e715f
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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26 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
937aa69e715f
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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27 #set read1 = "input_f.fastq.gz" |
|
937aa69e715f
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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28 #set compressed = "GZ" |
|
937aa69e715f
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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29 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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30 #set read1 = "input_f.fastq.bz2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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31 #set compressed = "BZ2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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32 #else: |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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33 #set read1 = "input_f.fastq" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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34 #end if |
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937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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35 ln -f -s '${library.input_1}' ${read1} && |
|
937aa69e715f
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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36 |
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937aa69e715f
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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37 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
937aa69e715f
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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38 #set read2 = "input_r.fastq.gz" |
|
937aa69e715f
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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39 #set compressed = "GZ" |
|
937aa69e715f
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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40 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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41 #set read2 = "input_r.fastq.bz2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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42 #set compressed = "BZ2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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43 #else: |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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44 #set read2 = "input_r.fastq" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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45 #end if |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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46 ln -f -s '${library.input_2}' ${read2} && |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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47 #else if str($library.type) == 'paired_collection': |
|
937aa69e715f
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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48 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
937aa69e715f
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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49 #set read1 = "input_f.fastq.gz" |
|
937aa69e715f
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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50 #set compressed = "GZ" |
|
937aa69e715f
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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51 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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52 #set read1 = "input_f.fastq.bz2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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53 #set compressed = "BZ2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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54 #else: |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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55 #set read1 = "input_f.fastq" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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56 #end if |
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937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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57 ln -s '${library.input_1.forward}' ${read1} && |
|
937aa69e715f
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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58 |
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937aa69e715f
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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59 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
937aa69e715f
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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60 #set read2 = "input_r.fastq.gz" |
|
937aa69e715f
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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61 #set compressed = "GZ" |
|
937aa69e715f
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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62 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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63 #set read2 = "input_r.fastq.bz2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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64 #set compressed = "BZ2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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65 #else: |
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937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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66 #set read2 = "input_r.fastq" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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67 #end if |
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937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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68 ln -s '${library.input_1.reverse}' ${read2} && |
|
937aa69e715f
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 #else: |
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937aa69e715f
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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70 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
|
937aa69e715f
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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71 #set read1 = "input_f.fastq.gz" |
|
937aa69e715f
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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72 #set compressed = "GZ" |
|
937aa69e715f
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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73 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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74 #set read1 = "input_f.fastq.bz2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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75 #set compressed = "BZ2" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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76 #else: |
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937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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77 #set read1 = "input_f.fastq" |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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78 #end if |
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937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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79 ln -s '${library.input_1}' ${read1} && |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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80 #end if |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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81 |
| 0 | 82 ## execute bowtie2 |
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7
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
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83 |
| 0 | 84 bowtie2 |
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7
4f92dccc808a
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85 |
| 0 | 86 ## number of threads |
| 87 -p \${GALAXY_SLOTS:-4} | |
| 88 | |
| 89 ## index file path | |
|
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90 -x '$index_path' |
|
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91 |
| 2 | 92 ## Fastq inputs |
| 93 #if str( $library.type ) == "single": | |
|
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94 -U '${read1}' |
| 2 | 95 #if str( $library.unaligned_file ) == "true": |
|
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96 #if $compressed == "GZ": |
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97 --un-gz '${output_unaligned_reads_l}' |
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98 #else if $compressed == "BZ2": |
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99 --un-bz2 '${output_unaligned_reads_l}' |
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100 #else: |
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101 --un '${output_unaligned_reads_l}' |
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102 #end if |
| 0 | 103 #end if |
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104 #if str( $library.aligned_file ) == "true": |
|
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105 #if $compressed == "GZ": |
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106 --al-gz '${output_aligned_reads_l}' |
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107 #else if $compressed == "BZ2": |
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108 --al-bz2 '${output_aligned_reads_l}' |
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109 #else: |
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110 --al '${output_aligned_reads_l}' |
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111 #end if |
|
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112 #end if |
|
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113 #else: |
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114 -1 '${read1}' |
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115 -2 '${read2}' |
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116 #if str( $library.unaligned_file ) == "true": |
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117 #if $compressed == "GZ": |
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118 --un-conc-gz '${output_unaligned_reads_l}' |
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119 #else if $compressed == "BZ2": |
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120 --un-conc-bz2 '${output_unaligned_reads_l}' |
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121 #else: |
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122 --un-conc '${output_unaligned_reads_l}' |
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123 #end if |
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124 #end if |
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125 #if str( $library.aligned_file ) == "true": |
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126 #if $compressed == "GZ": |
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127 --al-conc-gz '${output_aligned_reads_l}' |
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128 #else if $compressed == "BZ2": |
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129 --al-conc-bz2 '${output_aligned_reads_l}' |
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130 #else: |
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131 --al-conc '${output_aligned_reads_l}' |
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132 #end if |
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133 #end if |
| 2 | 134 #if str( $library.paired_options.paired_options_selector ) == "yes": |
| 135 -I "${library.paired_options.I}" | |
| 136 -X "${library.paired_options.X}" | |
| 137 ${library.paired_options.fr_rf_ff} | |
| 138 ${library.paired_options.no_mixed} | |
| 139 ${library.paired_options.no_discordant} | |
| 140 ${library.paired_options.dovetail} | |
| 141 ${library.paired_options.no_contain} | |
| 142 ${library.paired_options.no_overlap} | |
| 143 #end if | |
| 0 | 144 #end if |
|
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145 |
|
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146 ## Read group information. |
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147 @define_read_group_helpers@ |
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148 #if str( $library.type ) == "single": |
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149 #set $rg_auto_name = $read_group_name_default($library.input_1) |
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150 #elif str( $library.type ) == "paired": |
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151 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) |
|
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152 #else |
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153 #set $rg_auto_name = $read_group_name_default($library.input_1) |
|
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154 #end if |
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155 @set_use_rg_var@ |
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156 @set_read_group_vars@ |
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157 #if $use_rg |
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158 $format_read_group("", $rg_id, '"', arg='--rg-id ') |
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159 $format_read_group("SM:", $rg_sm, '"', arg='--rg ') |
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160 $format_read_group("PL:", $rg_pl, '"', arg='--rg ') |
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161 $format_read_group("LB:", $rg_lb, '"', arg='--rg ') |
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162 $format_read_group("CN:", $rg_cn, '"', arg='--rg ') |
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163 $format_read_group("DS:", $rg_ds, '"', arg='--rg ') |
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164 $format_read_group("DT:", $rg_dt, '"', arg='--rg ') |
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165 $format_read_group("FO:", $rg_fo, '"', arg='--rg ') |
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166 $format_read_group("KS:", $rg_ks, '"', arg='--rg ') |
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167 $format_read_group("PG:", $rg_pg, '"', arg='--rg ') |
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168 $format_read_group("PI:", $rg_pi, '"', arg='--rg ') |
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169 $format_read_group("PU:", $rg_pu, '"', arg='--rg ') |
| 2 | 170 #end if |
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171 |
| 2 | 172 ## Analysis type |
| 173 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ): | |
| 174 $analysis_type.presets | |
| 175 #elif str( $analysis_type.analysis_type_selector ) == "full": | |
| 176 #if str( $analysis_type.input_options.input_options_selector ) == "yes": | |
| 177 --skip "${analysis_type.input_options.skip}" | |
| 178 --qupto "${analysis_type.input_options.qupto}" | |
| 179 --trim5 "${analysis_type.input_options.trim5}" | |
| 180 --trim3 "${analysis_type.input_options.trim3}" | |
| 181 ${analysis_type.input_options.qv_encoding} | |
| 3 | 182 ${analysis_type.input_options.solexa_quals} |
| 183 ${analysis_type.input_options.int_quals} | |
| 0 | 184 #end if |
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185 |
| 2 | 186 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes": |
| 3 | 187 -N "${analysis_type.alignment_options.N}" |
| 188 -L "${analysis_type.alignment_options.L}" | |
| 189 -i "${analysis_type.alignment_options.i}" | |
| 190 --n-ceil "${analysis_type.alignment_options.n_ceil}" | |
| 191 --dpad "${analysis_type.alignment_options.dpad}" | |
| 192 --gbar "${analysis_type.alignment_options.gbar}" | |
| 193 ${analysis_type.alignment_options.ignore_quals} | |
| 2 | 194 ${analysis_type.alignment_options.nofw} |
| 195 ${analysis_type.alignment_options.norc} | |
| 196 ${analysis_type.alignment_options.no_1mm_upfront} | |
| 197 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end": | |
| 198 --end-to-end | |
| 3 | 199 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}" |
| 2 | 200 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local": |
| 201 --local | |
| 3 | 202 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}" |
| 2 | 203 #end if |
| 204 #end if | |
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205 |
| 2 | 206 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes": |
| 3 | 207 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ): |
| 208 --ma "${analysis_type.scoring_options.ma}" | |
| 209 #end if | |
| 2 | 210 --mp "${analysis_type.scoring_options.mp}" |
| 211 --np "${analysis_type.scoring_options.np}" | |
| 212 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}" | |
| 213 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}" | |
| 214 #end if | |
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215 |
| 2 | 216 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k": |
| 217 -k "${analysis_type.reporting_options.k}" | |
| 218 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a": | |
| 219 -a | |
| 220 #end if | |
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221 |
| 2 | 222 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": |
| 223 -D "${analysis_type.effort_options.D}" | |
| 224 -R "${analysis_type.effort_options.R}" | |
| 225 #end if | |
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226 |
| 2 | 227 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes": |
| 3 | 228 ${analysis_type.sam_options.no_unal} |
| 229 ${analysis_type.sam_options.omit_sec_seq} | |
| 2 | 230 #end if |
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231 |
| 2 | 232 #if str( $analysis_type.other_options.other_options_selector ) == "yes": |
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233 ${analysis_type.other_options.reorder} |
| 3 | 234 ${analysis_type.other_options.non_deterministic} |
| 2 | 235 --seed "${analysis_type.other_options.seed}" |
| 0 | 236 #end if |
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237 |
| 2 | 238 #elif str( $analysis_type.analysis_type_selector ) == "cline": |
| 239 ${analysis_type.cline} | |
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240 #end if |
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241 |
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242 ## mapping stats (i.e. stderr from bowtie2) |
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243 #if $save_mapping_stats |
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244 2> '$mapping_stats' |
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245 #end if |
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246 |
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247 ## output file |
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248 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ): |
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249 | samtools sort -O bam -o '$output' |
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250 #else |
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251 > '$output_sam' |
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252 #end if |
| 3 | 253 |
| 0 | 254 ## rename unaligned sequence files |
| 255 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: | |
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256 #from os.path import splitext |
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257 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) ) |
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258 && mv "${ _unaligned_root }.1${_unaligned_ext}" '$output_unaligned_reads_l' |
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259 && mv "${ _unaligned_root }.2${_unaligned_ext}" '$output_unaligned_reads_r' |
| 0 | 260 #end if |
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261 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r: |
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262 #from os.path import splitext |
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263 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) ) |
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264 && mv "${ _aligned_root }.1${_aligned_ext}" '$output_aligned_reads_l' |
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265 && mv "${ _aligned_root }.2${_aligned_ext}" '$output_aligned_reads_r' |
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266 #end if |
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267 |
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268 ]]></command> |
| 0 | 269 <inputs> |
| 270 <!-- single/paired --> | |
| 271 <conditional name="library"> | |
| 2 | 272 <param name="type" type="select" label="Is this single or paired library"> |
| 0 | 273 <option value="single">Single-end</option> |
| 274 <option value="paired">Paired-end</option> | |
| 2 | 275 <option value="paired_collection">Paired-end Dataset Collection</option> |
| 0 | 276 </param> |
| 2 | 277 |
| 0 | 278 <when value="single"> |
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279 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file" help="Must be of datatype "fastqsanger"" /> |
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280 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" /> |
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281 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" /> |
| 0 | 282 </when> |
| 283 <when value="paired"> | |
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284 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> |
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285 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> |
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286 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" /> |
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287 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" /> |
| 2 | 288 <conditional name="paired_options"> |
| 289 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See "Alignment Options" section of Help below for information"> | |
| 290 <option value="no" selected="True">No</option> | |
| 291 <option value="yes">Yes</option> | |
| 292 </param> | |
| 293 <when value="yes"> | |
| 294 <param name="I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" help="-I/--minins; E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/> | |
| 3 | 295 <param name="X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" help="-X/--maxins; E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/> |
| 296 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)"> | |
| 2 | 297 <option value="--fr" selected="True">--fr</option> |
| 3 | 298 <option value="--rf">--rf</option> |
| 2 | 299 <option value="--ff">--ff</option> |
| 300 </param> | |
| 301 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/> | |
| 302 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/> | |
| 3 | 303 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/> |
|
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304 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/> |
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305 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/> |
| 2 | 306 </when> |
| 307 <when value="no"> | |
| 308 <!-- do nothing --> | |
| 309 </when> | |
| 310 </conditional> | |
| 311 </when> | |
| 312 <when value="paired_collection"> | |
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313 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger"" /> |
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314 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" /> |
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315 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" /> |
| 2 | 316 <conditional name="paired_options"> |
| 317 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See "Alignment Options" section of Help below for information"> | |
| 318 <option value="no" selected="True">No</option> | |
| 319 <option value="yes">Yes</option> | |
| 320 </param> | |
| 321 <when value="yes"> | |
| 322 <param name="I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" help="-I/--minins; E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/> | |
| 3 | 323 <param name="X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" help="-X/--maxins; E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/> |
| 324 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)"> | |
| 2 | 325 <option value="--fr" selected="True">--fr</option> |
| 3 | 326 <option value="--rf">--rf</option> |
| 2 | 327 <option value="--ff">--ff</option> |
| 328 </param> | |
| 329 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/> | |
| 330 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/> | |
| 3 | 331 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/> |
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332 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/> |
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333 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/> |
| 2 | 334 </when> |
| 335 <when value="no"> | |
| 336 <!-- do nothing --> | |
| 337 </when> | |
| 338 </conditional> | |
| 0 | 339 </when> |
| 340 </conditional> | |
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341 |
| 0 | 342 <!-- reference genome --> |
| 343 <conditional name="reference_genome"> | |
| 2 | 344 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> |
| 345 <option value="indexed">Use a built-in genome index</option> | |
| 346 <option value="history">Use a genome from the history and build index</option> | |
| 0 | 347 </param> |
| 348 <when value="indexed"> | |
| 2 | 349 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
| 0 | 350 <options from_data_table="bowtie2_indexes"> |
| 351 <filter type="sort_by" column="2"/> | |
| 352 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 353 </options> | |
| 354 </param> | |
| 355 </when> | |
| 356 <when value="history"> | |
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357 <param name="own_file" type="data" format="fasta" label="Select reference genome" /> |
| 0 | 358 </when> |
| 359 </conditional> | |
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360 |
| 2 | 361 <!-- read group settings --> |
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362 <expand macro="read_group_conditional" /> |
| 2 | 363 <conditional name="analysis_type"> |
| 364 <param name="analysis_type_selector" type="select" label="Select analysis mode"> | |
| 365 <option value="simple">1: Default setting only</option> | |
| 366 <option value="full">2: Full parameter list</option> | |
| 0 | 367 </param> |
| 2 | 368 <when value="simple"> |
| 369 <param name="presets" type="select" display="radio" label="Do you want to use presets?" help="Allow selecting among several preset parameter settings. Choosing between these will result in dramatic changes in runtime. See help below to understand effects of these presets."> | |
| 370 <option value="no_presets" selected="True">No, just use defaults</option> | |
| 371 <option value="--very-fast">Very fast end-to-end (--very-fast)</option> | |
| 372 <option value="--fast">Fast end-to-end (--fast)</option> | |
| 373 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option> | |
| 374 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option> | |
| 375 <option value="--very-fast-local">Very fast local (--very-fast-local)</option> | |
| 376 <option value="--fast-local">Fast local (--fast-local)</option> | |
| 377 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option> | |
| 378 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option> | |
| 0 | 379 </param> |
| 2 | 380 </when> |
| 381 <when value="full"> | |
| 382 <conditional name="input_options"> | |
| 383 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See "Input Options" section of Help below for information"> | |
| 384 <option value="yes">Yes</option> | |
| 385 <option value="no" selected="true">No</option> | |
| 386 </param> | |
| 387 <when value="yes"> | |
| 3 | 388 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/> |
| 389 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/> | |
| 2 | 390 <param name="trim5" type="integer" min="0" value="0" label="Trim that many bases from 5' (left) end of each read before alignment" help="-5/--trim5; default=0"/> |
| 391 <param name="trim3" type="integer" min="0" value="0" label="Trim that many bases from 3' (right) end of each read before alignment" help="-3/--trim3; default=0"/> | |
| 392 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details"> | |
| 3 | 393 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option> |
| 394 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option> | |
| 2 | 395 </param> |
| 3 | 396 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/> |
| 397 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/> | |
| 2 | 398 </when> |
| 399 <when value="no"> | |
| 400 <!-- do nothing --> | |
| 401 </when> | |
| 402 </conditional> | |
| 403 <conditional name="alignment_options"> | |
| 404 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See "Alignment Options" section of Help below for information"> | |
| 405 <option value="yes">Yes</option> | |
| 406 <option value="no" selected="true">No</option> | |
| 407 </param> | |
| 408 <when value="yes"> | |
| 409 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/> | |
| 3 | 410 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/> |
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411 <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/> |
| 3 | 412 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/> |
| 413 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/> | |
| 2 | 414 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/> |
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415 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/> |
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416 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/> |
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417 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/> |
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418 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/> |
| 2 | 419 <conditional name="align_mode"> |
| 420 <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end"> | |
| 421 <option value="end-to-end" selected="True">End to End (--end-to-end)</option> | |
| 422 <option value="local">Local (--local)</option> | |
| 423 </param> | |
| 424 <when value="end-to-end"> | |
| 3 | 425 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/> |
| 2 | 426 </when> |
| 427 <when value="local"> | |
| 3 | 428 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/> |
| 2 | 429 </when> |
| 430 </conditional> | |
| 431 </when> | |
| 432 <when value="no"> | |
| 433 <!-- do nothing --> | |
| 434 </when> | |
| 435 </conditional> | |
| 436 <conditional name="scoring_options"> | |
| 437 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See "Scoring Options" section of Help below for information"> | |
| 438 <option value="yes">Yes</option> | |
| 439 <option value="no" selected="true">No</option> | |
| 440 </param> | |
| 441 <when value="yes"> | |
| 442 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma; In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/> | |
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443 <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/> |
| 2 | 444 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/> |
| 445 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/> | |
| 446 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/> | |
| 447 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/> | |
| 448 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/> | |
| 449 </when> | |
| 450 <when value="no"> | |
| 451 <!-- do nothing --> | |
| 452 </when> | |
| 453 </conditional> | |
| 454 <conditional name="reporting_options"> | |
| 455 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See "Reporting Options" section of Help below for information on -k and -a options"> | |
| 456 <option value="no" selected="true">No, do not set</option> | |
| 457 <option value="k">Set -k option and enter -k value</option> | |
| 458 <option value="a">Set -a option</option> | |
| 459 </param> | |
| 460 <when value="no"> | |
| 461 <!-- do nothing --> | |
| 462 </when> | |
| 3 | 463 <when value="k"> |
| 464 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/> | |
| 2 | 465 </when> |
| 3 | 466 <when value="a"> |
| 2 | 467 <!-- do nothing here; set -a flag on the command line--> |
| 468 </when> | |
| 469 </conditional> | |
| 470 <conditional name="effort_options"> | |
| 471 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See "Effort Options" section of Help below for information"> | |
| 472 <option value="yes">Yes</option> | |
| 473 <option value="no" selected="true">No</option> | |
| 474 </param> | |
| 475 <when value="yes"> | |
| 3 | 476 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/> |
| 2 | 477 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/> |
| 478 </when> | |
| 479 <when value="no"> | |
| 480 <!-- do nothing --> | |
| 481 </when> | |
| 482 </conditional> | |
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483 |
| 2 | 484 <conditional name="sam_options"> |
| 485 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See "Output Options" section of Help below for information"> | |
| 486 <option value="yes">Yes</option> | |
| 487 <option value="no" selected="true">No</option> | |
| 488 </param> | |
| 489 <when value="yes"> | |
| 3 | 490 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/> |
| 491 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/> | |
| 2 | 492 </when> |
| 493 <when value="no"> | |
| 494 <!-- do nothing --> | |
| 495 </when> | |
| 496 </conditional> | |
| 497 <conditional name="other_options"> | |
| 498 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See "Other Options" section of Help below for information"> | |
| 499 <option value="yes">Yes</option> | |
| 500 <option value="no" selected="true">No</option> | |
| 501 </param> | |
| 502 <when value="yes"> | |
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503 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file" help="--reorder; Default=False"/> |
| 2 | 504 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/> |
| 3 | 505 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/> |
| 2 | 506 </when> |
| 507 <when value="no"> | |
| 508 <!-- do nothing --> | |
| 509 </when> | |
| 510 </conditional> | |
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511 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/> |
| 0 | 512 </when> |
| 513 </conditional> | |
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514 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" /> |
| 0 | 515 </inputs> |
| 516 | |
| 517 <!-- define outputs --> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
518 |
| 0 | 519 <outputs> |
|
11
b4e9cf5f2ae8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
520 |
| 0 | 521 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > |
| 2 | 522 <filter>library['unaligned_file'] is True</filter> |
| 0 | 523 <actions> |
|
7
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
524 <conditional name="library.type"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
525 <when value="single"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
526 <action type="format"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
527 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
528 </action> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
529 </when> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
530 <when value="paired"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
531 <action type="format"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
532 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
533 </action> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
534 </when> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
535 <when value="paired_collection"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
536 <action type="format"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
537 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
538 </action> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
539 </when> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
540 </conditional> |
| 0 | 541 </actions> |
| 542 </data> | |
|
10
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
543 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" > |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
544 <filter>library['aligned_file'] is True</filter> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
545 <actions> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
546 <conditional name="library.type"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
547 <when value="single"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
548 <action type="format"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
549 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
550 </action> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
551 </when> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
552 <when value="paired"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
553 <action type="format"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
554 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
555 </action> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
556 </when> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
557 <when value="paired_collection"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
558 <action type="format"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
559 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
560 </action> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
561 </when> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
562 </conditional> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
563 </actions> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
564 </data> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
565 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
566 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
567 <actions> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
568 <conditional name="library.type"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
569 <when value="paired"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
570 <action type="format"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
571 <option type="from_param" name="library.input_2" param_attribute="ext" /> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
572 </action> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
573 </when> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
574 <when value="paired_collection"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
575 <action type="format"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
576 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
577 </action> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
578 </when> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
579 </conditional> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
580 </actions> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents:
8
diff
changeset
|
581 </data> |
| 0 | 582 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> |
| 2 | 583 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter> |
| 0 | 584 <actions> |
|
7
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
585 <conditional name="library.type"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
586 <when value="paired"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
587 <action type="format"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
588 <option type="from_param" name="library.input_2" param_attribute="ext" /> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
589 </action> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
590 </when> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
591 <when value="paired_collection"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
592 <action type="format"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
593 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
594 </action> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
595 </when> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
596 </conditional> |
| 0 | 597 </actions> |
| 598 </data> | |
|
11
b4e9cf5f2ae8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
599 |
| 3 | 600 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)"> |
|
7
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
601 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
602 <actions> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
603 <conditional name="reference_genome.source"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
604 <when value="indexed"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
6
diff
changeset
|
605 <action type="metadata" name="dbkey"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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diff
changeset
|
606 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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diff
changeset
|
607 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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diff
changeset
|
608 <filter type="param_value" ref="reference_genome.index" column="0"/> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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diff
changeset
|
609 </option> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
610 </action> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
611 </when> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
612 <when value="history"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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diff
changeset
|
613 <action type="metadata" name="dbkey"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
614 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
615 </action> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
616 </when> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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diff
changeset
|
617 </conditional> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
618 </actions> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
619 </data> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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diff
changeset
|
620 |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
621 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)"> |
|
4f92dccc808a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
|
622 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter> |
| 0 | 623 <actions> |
| 624 <conditional name="reference_genome.source"> | |
| 625 <when value="indexed"> | |
| 626 <action type="metadata" name="dbkey"> | |
| 627 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> | |
| 628 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | |
| 629 <filter type="param_value" ref="reference_genome.index" column="0"/> | |
| 630 </option> | |
| 631 </action> | |
| 632 </when> | |
| 633 <when value="history"> | |
| 634 <action type="metadata" name="dbkey"> | |
| 635 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> | |
| 636 </action> | |
| 637 </when> | |
| 638 </conditional> | |
| 639 </actions> | |
| 640 </data> | |
|
10
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents:
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diff
changeset
|
641 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats"> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents:
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diff
changeset
|
642 <filter>save_mapping_stats is True</filter> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents:
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changeset
|
643 </data> |
| 3 | 644 |
| 0 | 645 </outputs> |
| 646 | |
| 647 <tests> | |
| 648 <test> | |
| 649 <!-- basic test on single paired default run --> | |
| 2 | 650 <param name="type" value="paired"/> |
| 0 | 651 <param name="selection" value="no"/> |
| 2 | 652 <param name="paired_options_selector" value="no"/> |
| 0 | 653 <param name="unaligned_file" value="false"/> |
| 2 | 654 <param name="analysis_type_selector" value="simple"/> |
| 0 | 655 <param name="source" value="history" /> |
| 2 | 656 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
| 657 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> | |
| 658 <param name="own_file" value="bowtie2-ref.fasta" /> | |
| 659 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | |
| 0 | 660 </test> |
|
5
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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diff
changeset
|
661 <test> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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changeset
|
662 <!-- basic test on single paired default run --> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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changeset
|
663 <param name="type" value="paired"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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diff
changeset
|
664 <param name="selection" value="no"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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diff
changeset
|
665 <param name="paired_options_selector" value="no"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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changeset
|
666 <param name="unaligned_file" value="false"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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|
667 <param name="analysis_type_selector" value="simple"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
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diff
changeset
|
668 <param name="rg_selector" value="set"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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changeset
|
669 <param name="ID" value="rg1"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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changeset
|
670 <param name="PL" value="CAPILLARY"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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changeset
|
671 <param name="source" value="history" /> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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changeset
|
672 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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diff
changeset
|
673 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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|
674 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents:
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|
675 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> |
|
42bb952b4e3c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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676 </test> |
|
10
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents:
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changeset
|
677 <test> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents:
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changeset
|
678 <!-- basic test on single paired default run with stats--> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents:
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diff
changeset
|
679 <param name="type" value="paired"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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changeset
|
680 <param name="selection" value="no"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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changeset
|
681 <param name="paired_options_selector" value="no"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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changeset
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682 <param name="unaligned_file" value="false"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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683 <param name="analysis_type_selector" value="simple"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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changeset
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684 <param name="source" value="history" /> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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changeset
|
685 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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686 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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687 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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changeset
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688 <param name="save_mapping_stats" value="true" /> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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changeset
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689 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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690 <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/> |
|
a9d4f71dbfb0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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691 </test> |
|
14
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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692 <test> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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693 <!-- test fastqsanger.gz input --> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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694 <param name="type" value="paired"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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695 <param name="selection" value="no"/> |
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937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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696 <param name="paired_options_selector" value="no"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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697 <param name="unaligned_file" value="false"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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698 <param name="analysis_type_selector" value="simple"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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699 <param name="source" value="history" /> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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700 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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701 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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702 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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703 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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704 </test> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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705 <test> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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706 <!-- test fastqsanger.bz2 input --> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
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707 <param name="type" value="paired"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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changeset
|
708 <param name="selection" value="no"/> |
|
937aa69e715f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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709 <param name="paired_options_selector" value="no"/> |
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710 <param name="unaligned_file" value="false"/> |
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711 <param name="analysis_type_selector" value="simple"/> |
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712 <param name="source" value="history" /> |
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713 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> |
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714 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> |
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715 <param name="own_file" value="bowtie2-ref.fasta" /> |
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716 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> |
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717 </test> |
| 0 | 718 </tests> |
| 719 | |
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720 <help><![CDATA[ |
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721 |
| 0 | 722 **Bowtie2 Overview** |
|
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723 |
| 2 | 724 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. |
| 725 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead. | |
| 726 | |
| 727 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/ | |
| 728 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml | |
| 729 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf | |
| 730 | |
| 731 ----- | |
| 0 | 732 |
| 2 | 733 **Selecting reference genomes for Bowtie2** |
| 734 | |
| 735 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 | 736 |
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737 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 | 738 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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739 |
| 2 | 740 If your genome of interest is not listed here you have two choices: |
| 741 | |
| 742 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 | |
| 743 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 | 744 |
| 745 ------ | |
| 746 | |
| 2 | 747 .. class:: infomark |
| 748 | |
| 749 **Bowtie2 options** | |
| 750 | |
| 751 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below. | |
| 752 | |
| 753 ----- | |
| 754 | |
| 0 | 755 **Inputs** |
| 756 | |
| 757 Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files. | |
| 758 | |
| 759 ------ | |
| 760 | |
| 2 | 761 **Input options**:: |
| 762 | |
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763 -s/--skip <int> |
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764 Skip (i.e. do not align) the first `<int>` reads or pairs in the input. |
| 2 | 765 |
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766 -u/--qupto <int> |
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767 Align the first `<int>` reads or read pairs from the input (after the |
| 2 | 768 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit. |
| 769 | |
|
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770 -5/--trim5 <int> |
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771 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0). |
| 0 | 772 |
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773 -3/--trim3 <int> |
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774 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0). |
| 2 | 775 |
| 776 --phred33 | |
| 777 Input qualities are ASCII chars equal to the Phred quality plus 33. This is | |
| 778 also called the "Phred+33" encoding, which is used by the very latest Illumina | |
| 779 pipelines. | |
| 780 | |
| 781 --phred64 | |
| 3 | 782 Input qualities are ASCII chars equal to the Phred quality plus 64. This is |
| 2 | 783 also called the "Phred+64" encoding. |
| 0 | 784 |
| 2 | 785 --solexa-quals |
| 786 Convert input qualities from Solexa Phred quality (which can be negative) to | |
| 787 Phred Phred quality (which can't). This scheme was used in older Illumina GA | |
| 788 Pipeline versions (prior to 1.3). Default: off. | |
| 789 | |
| 790 --int-quals | |
| 791 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`.... | |
| 3 | 792 Integers are treated as being on the Phred quality scale unless |
| 2 | 793 `--solexa-quals` is also specified. Default: off. |
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794 |
| 2 | 795 ------ |
| 796 | |
| 797 **Presets in `--end-to-end` mode**:: | |
| 798 | |
| 799 --very-fast | |
| 800 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50` | |
| 801 | |
| 802 --fast | |
| 803 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50` | |
|
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804 |
| 2 | 805 --sensitive |
| 806 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode) | |
| 807 | |
| 808 --very-sensitive | |
| 809 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
| 0 | 810 |
| 811 ------ | |
| 812 | |
| 2 | 813 **Presets options in `--local` mode**:: |
| 0 | 814 |
| 2 | 815 --very-fast-local |
| 816 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00` | |
| 0 | 817 |
| 2 | 818 --fast-local |
| 819 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75` | |
| 0 | 820 |
| 2 | 821 --sensitive-local |
| 822 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode) | |
| 0 | 823 |
| 2 | 824 --very-sensitive-local |
| 825 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
|
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826 |
| 0 | 827 ------ |
| 828 | |
| 2 | 829 **Alignment options**:: |
| 830 | |
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831 -N <int> |
| 3 | 832 Sets the number of mismatches to allowed in a seed alignment during multiseed |
| 833 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower | |
| 2 | 834 (often much slower) but increases sensitivity. Default: 0. |
| 835 | |
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836 -L <int> |
| 3 | 837 Sets the length of the seed substrings to align during multiseed alignment. |
| 838 Smaller values make alignment slower but more sensitive. Default: the | |
| 839 `--sensitive` preset is used by default, which sets `-L` to 22 in | |
| 840 `--end-to-end` mode and to 20 in `--local` mode. | |
| 2 | 841 |
|
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842 -i <func> |
| 2 | 843 Sets a function governing the interval between seed substrings to use during |
| 3 | 844 multiseed alignment. For instance, if the read has 30 characers, and seed |
| 2 | 845 length is 10, and the seed interval is 6, the seeds extracted will be: |
| 846 | |
| 847 Read: TAGCTACGCTCTACGCTATCATGCATAAAC | |
| 848 Seed 1 fw: TAGCTACGCT | |
| 849 Seed 1 rc: AGCGTAGCTA | |
| 850 Seed 2 fw: CGCTCTACGC | |
| 851 Seed 2 rc: GCGTAGAGCG | |
| 852 Seed 3 fw: ACGCTATCAT | |
| 853 Seed 3 rc: ATGATAGCGT | |
| 854 Seed 4 fw: TCATGCATAA | |
| 855 Seed 4 rc: TTATGCATGA | |
| 856 | |
| 857 Since it's best to use longer intervals for longer reads, this parameter sets | |
| 858 the interval as a function of the read length, rather than a single | |
| 859 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the | |
| 860 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. | |
| 3 | 861 If the function returns a result less than |
| 2 | 862 1, it is rounded up to 1. Default: the `--sensitive` preset is used by |
| 863 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75` | |
| 864 in `--local` mode. | |
| 865 | |
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866 --n-ceil <func> |
| 2 | 867 Sets a function governing the maximum number of ambiguous characters (usually |
| 868 `N`s and/or `.`s) allowed in a read as a function of read length. For instance, | |
| 869 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, | |
| 3 | 870 where x is the read length. Reads exceeding this ceiling are filtered out. |
| 871 Default: `L,0,0.15`. | |
| 2 | 872 |
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873 --dpad <int> |
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874 "Pads" dynamic programming problems by `<int>` columns on either side to allow |
| 2 | 875 gaps. Default: 15. |
| 876 | |
|
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877 --gbar <int> |
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878 Disallow gaps within `<int>` positions of the beginning or end of the read. |
| 2 | 879 Default: 4. |
| 880 | |
| 881 --ignore-quals | |
| 882 When calculating a mismatch penalty, always consider the quality value at the | |
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883 mismatched position to be the highest possible, regardless of the actual value. |
| 2 | 884 I.e. input is treated as though all quality values are high. This is also the |
| 885 default behavior when the input doesn't specify quality values (e.g. in `-f`, | |
| 886 `-r`, or `-c` modes). | |
| 0 | 887 |
| 2 | 888 --nofw/--norc |
| 889 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to | |
| 890 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will | |
| 891 not attempt to align unpaired reads against the reverse-complement (Crick) | |
| 892 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the | |
| 893 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those | |
| 894 paired-end configurations corresponding to fragments from the reverse-complement | |
|
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895 (Crick) strand. Default: both strands enabled. |
| 2 | 896 |
| 897 --no-1mm-upfront | |
| 898 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch | |
| 3 | 899 end-to-end alignment for the read *before* trying the multiseed heuristic. Such |
| 2 | 900 alignments can be found very quickly, and many short read alignments have exact or |
| 901 near-exact end-to-end alignments. However, this can lead to unexpected | |
| 3 | 902 alignments when the user also sets options governing the multiseed heuristic, |
| 2 | 903 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal |
| 904 to the length of the read, the user will be surprised to find 1-mismatch alignments | |
| 905 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end | |
| 3 | 906 alignments before using the multiseed heuristic, which leads to the expected |
| 2 | 907 behavior when combined with options such as `-L` and `-N`. This comes at the |
| 908 expense of speed. | |
| 909 | |
| 910 --end-to-end | |
| 911 In this mode, Bowtie 2 requires that the entire read align from one end to the | |
| 912 other, without any trimming (or "soft clipping") of characters from either end. | |
| 913 The match bonus `--ma` always equals 0 in this mode, so all alignment scores | |
| 914 are less than or equal to 0, and the greatest possible alignment score is 0. | |
| 915 This is mutually exclusive with `--local`. `--end-to-end` is the default mode. | |
| 0 | 916 |
| 2 | 917 --local |
| 918 In this mode, Bowtie 2 does not require that the entire read align from one end | |
| 919 to the other. Rather, some characters may be omitted ("soft clipped") from the | |
| 920 ends in order to achieve the greatest possible alignment score. The match bonus | |
| 921 `--ma` is used in this mode, and the best possible alignment score is equal to | |
| 922 the match bonus (`--ma`) times the length of the read. Specifying `--local` | |
| 923 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying | |
| 924 the local version of the preset (`--very-fast-local`). This is mutually | |
| 925 exclusive with `--end-to-end`. `--end-to-end` is the default mode. | |
|
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926 |
| 2 | 927 ----- |
| 928 | |
| 929 **Scoring options**:: | |
| 930 | |
|
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931 --ma <int> |
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932 Sets the match bonus. In `--local` mode `<int>` is added to the alignment |
| 2 | 933 score for each position where a read character aligns to a reference character |
| 934 and the characters match. Not used in `--end-to-end` mode. Default: 2. | |
| 935 | |
| 936 --mp MX,MN | |
| 937 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A | |
| 938 number less than or equal to `MX` and greater than or equal to `MN` is | |
| 939 subtracted from the alignment score for each position where a read character | |
| 940 aligns to a reference character, the characters do not match, and neither is an | |
| 941 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. | |
| 942 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` | |
| 943 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2. | |
| 944 | |
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945 --np <int> |
| 2 | 946 Sets penalty for positions where the read, reference, or both, contain an |
| 947 ambiguous character such as `N`. Default: 1. | |
| 948 | |
|
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949 --rdg <int1>,<int2> |
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950 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of |
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951 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3. |
| 2 | 952 |
|
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953 --rfg <int1>,<int2> |
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954 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A |
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955 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default: |
| 2 | 956 5, 3. |
| 0 | 957 |
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958 --score-min <func> |
| 2 | 959 Sets a function governing the minimum alignment score needed for an alignment to |
| 960 be considered "valid" (i.e. good enough to report). This is a function of read | |
| 961 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` | |
| 3 | 962 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 | 963 the default in `--local` mode is `G,20,8`. |
|
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964 |
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965 ----- |
| 2 | 966 |
| 967 **Reporting options**:: | |
| 968 | |
|
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969 -k <int> |
| 2 | 970 By default, `bowtie2` searches for distinct, valid alignments for each read. |
| 971 When it finds a valid alignment, it continues looking for alignments that are | |
| 972 nearly as good or better. The best alignment found is reported (randomly | |
| 973 selected from among best if tied). Information about the best alignments is | |
| 974 used to estimate mapping quality and to set SAM optional fields, such as | |
| 975 `AS:i` and `XS:i`. | |
| 976 | |
| 977 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it | |
|
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978 searches for at most `<int>` distinct, valid alignments for each read. The |
| 2 | 979 search terminates when it can't find more distinct valid alignments, or when it |
|
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980 finds `<int>`, whichever happens first. All alignments found are reported in |
| 2 | 981 descending order by alignment score. The alignment score for a paired-end |
| 982 alignment equals the sum of the alignment scores of the individual mates. Each | |
| 983 reported read or pair alignment beyond the first has the SAM 'secondary' bit | |
| 984 (which equals 256) set in its FLAGS field. For reads that have more than | |
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985 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the |
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986 `<int>` alignments reported are the best possible in terms of alignment score. |
| 2 | 987 `-k` is mutually exclusive with `-a`. |
| 0 | 988 |
| 2 | 989 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when |
| 990 aligning reads to long, repetitive genomes large `-k` can be very, very slow. | |
| 991 | |
| 992 -a | |
| 993 Like `-k` but with no upper limit on number of alignments to search for. `-a` | |
| 994 is mutually exclusive with `-k`. | |
| 995 | |
| 996 Note: Bowtie 2 is not designed with `-a` mode in mind, and when | |
| 997 aligning reads to long, repetitive genomes this mode can be very, very slow. | |
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998 |
| 2 | 999 ----- |
| 1000 | |
| 1001 **Effort options**:: | |
| 1002 | |
|
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1003 -D <int> |
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1004 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2 |
| 2 | 1005 moves on, using the alignments found so far. A seed extension "fails" if it |
| 1006 does not yield a new best or a new second-best alignment. This limit is | |
| 1007 automatically adjusted up when -k or -a are specified. Default: 15. | |
| 1008 | |
|
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1009 -R <int> |
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1010 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with |
| 2 | 1011 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads |
| 1012 (same length, same number of mismatches allowed) at different offsets and | |
| 1013 searches for more alignments. A read is considered to have repetitive seeds if | |
| 1014 the total number of seed hits divided by the number of seeds that aligned at | |
| 1015 least once is greater than 300. Default: 2. | |
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1016 |
| 2 | 1017 ----- |
| 1018 | |
| 1019 **Paired-end options**:: | |
| 0 | 1020 |
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1021 -I/--minins <int> |
| 2 | 1022 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is |
| 1023 specified and a paired-end alignment consists of two 20-bp alignments in the | |
| 1024 appropriate orientation with a 20-bp gap between them, that alignment is | |
| 1025 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not | |
| 1026 be valid in that case. If trimming options `-3` or `-5` are also used, the | |
| 1027 `-I` constraint is applied with respect to the untrimmed mates. | |
| 1028 | |
| 1029 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
| 1030 run. This is because larger differences bewteen `-I` and `-X` require that | |
| 1031 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
| 1032 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
| 1033 efficient. | |
| 1034 | |
|
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1035 Default: 0 (essentially imposing no minimum) |
| 2 | 1036 |
|
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1037 -X/--maxins <int> |
| 2 | 1038 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100` |
| 1039 is specified and a paired-end alignment consists of two 20-bp alignments in the | |
| 1040 proper orientation with a 60-bp gap between them, that alignment is considered | |
| 1041 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in | |
| 1042 that case. If trimming options `-3` or `-5` are also used, the `-X` | |
| 1043 constraint is applied with respect to the untrimmed mates, not the trimmed | |
| 1044 mates. | |
| 1045 | |
| 1046 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
| 1047 run. This is because larger differences bewteen `-I` and `-X` require that | |
| 1048 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
| 1049 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
| 1050 efficient. | |
| 1051 | |
| 1052 Default: 500. | |
| 0 | 1053 |
| 2 | 1054 --fr/--rf/--ff |
| 1055 The upstream/downstream mate orientations for a valid paired-end alignment | |
| 1056 against the forward reference strand. E.g., if `--fr` is specified and there is | |
| 1057 a candidate paired-end alignment where mate 1 appears upstream of the reverse | |
| 1058 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are | |
| 1059 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse | |
| 1060 complement of mate 1 and all other constraints are met, that too is valid. | |
| 1061 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a | |
| 1062 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1 | |
| 1063 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate | |
| 1064 for Illumina's Paired-end Sequencing Assay). | |
| 1065 | |
| 1066 --no-mixed | |
| 1067 By default, when `bowtie2` cannot find a concordant or discordant alignment for | |
| 1068 a pair, it then tries to find alignments for the individual mates. This option | |
| 1069 disables that behavior. | |
| 0 | 1070 |
| 2 | 1071 --no-discordant |
| 1072 By default, `bowtie2` looks for discordant alignments if it cannot find any | |
| 1073 concordant alignments. A discordant alignment is an alignment where both mates | |
| 1074 align uniquely, but that does not satisfy the paired-end constraints | |
| 1075 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior. | |
| 1076 | |
| 1077 --dovetail | |
| 1078 If the mates "dovetail", that is if one mate alignment extends past the | |
| 1079 beginning of the other such that the wrong mate begins upstream, consider that | |
| 3 | 1080 to be concordant. Default: mates cannot dovetail in a concordant alignment. |
| 2 | 1081 |
| 1082 --no-contain | |
| 1083 If one mate alignment contains the other, consider that to be non-concordant. | |
| 3 | 1084 Default: a mate can contain the other in a concordant alignment. |
| 2 | 1085 |
| 1086 --no-overlap | |
| 1087 If one mate alignment overlaps the other at all, consider that to be | |
| 3 | 1088 non-concordant. Default: mates can overlap in a concordant alignment. |
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1089 |
| 0 | 1090 ------ |
| 1091 | |
| 2 | 1092 **SAM options**:: |
| 0 | 1093 |
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1094 --rg-id <text> |
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1095 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be |
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1096 printed, with `<text>` as the value associated with the `ID:` tag. It also |
| 2 | 1097 causes the `RG:Z:` extra field to be attached to each SAM output record, with |
|
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1098 value set to `<text>`. |
| 0 | 1099 |
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1100 --rg <text> |
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1101 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the |
| 2 | 1102 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id` |
| 3 | 1103 must also be specified. This is because the `ID` tag is required by the SAM |
| 1104 Specification. Specify `--rg` multiple times to set multiple fields. See the | |
| 1105 SAM Specification for details about what fields are legal. | |
| 0 | 1106 |
| 2 | 1107 --omit-sec-seq |
| 1108 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ` | |
| 1109 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix | |
| 1110 in those fields instead. | |
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1111 |
| 2 | 1112 ----- |
| 0 | 1113 |
| 2 | 1114 **Other options**:: |
| 0 | 1115 |
| 2 | 1116 --reorder |
| 1117 Guarantees that output SAM records are printed in an order corresponding to the | |
| 1118 order of the reads in the original input file, even when `-p` is set greater | |
| 1119 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie | |
| 1120 2 to run somewhat slower and use somewhat more memory then if `--reorder` were | |
| 1121 not specified. Has no effect if `-p` is set to 1, since output order will | |
| 1122 naturally correspond to input order in that case. | |
| 0 | 1123 |
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1124 --seed <int> |
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1125 Use `<int>` as the seed for pseudo-random number generator. Default: 0. |
| 0 | 1126 |
| 2 | 1127 --non-deterministic |
| 1128 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It | |
| 1129 seeds the generator with a number derived from (a) the read name, (b) the | |
| 1130 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed` | |
| 1131 option. This means that if two reads are identical (same name, same | |
| 1132 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s) | |
| 1133 for both, even if there was ambiguity. When `--non-deterministic` is specified, | |
| 1134 Bowtie 2 re-initializes its pseudo-random generator for each read using the | |
| 1135 current time. This means that Bowtie 2 will not necessarily report the same | |
| 1136 alignment for two identical reads. This is counter-intuitive for some users, | |
| 1137 but might be more appropriate in situations where the input consists of many | |
| 1138 identical reads. | |
| 0 | 1139 |
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1140 ]]></help> |
| 2 | 1141 <citations> |
| 1142 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> | |
| 1143 <citation type="doi">10.1038/nmeth.1923</citation> | |
| 1144 </citations> | |
| 0 | 1145 </tool> |