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annotate bowtie2_wrapper.xml @ 29:f6877ad76b00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
author iuc
date Wed, 06 Jul 2022 10:26:09 +0000
parents cd659e8cc5fa
children 03e9b2fbc005
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f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
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1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy1" profile="20.05">
2
c1ec08cb34f9 Uploaded
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2 <description>- map reads against reference genome</description>
29
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
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3 <macros>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
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4 <import>bowtie2_macros.xml</import>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
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5 </macros>
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cd659e8cc5fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
iuc
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6 <xrefs>
cd659e8cc5fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
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7 <xref type="bio.tools">bowtie2</xref>
cd659e8cc5fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
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8 </xrefs>
11
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9 <requirements>
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09b2cdb7ace5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
iuc
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10 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
28
cd659e8cc5fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
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11 <requirement type="package" version="1.14">samtools</requirement>
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b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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12 </requirements>
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13 <version_command>bowtie2 --version</version_command>
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b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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14 <command detect_errors="exit_code"><![CDATA[
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3ba8d4563129 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
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15 ## Use pipefail if available to quit with first non-zero exit code
3ba8d4563129 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
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16 set -o | grep -q pipefail && set -o pipefail;
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iuc
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17 ## prepare bowtie2 index
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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18 #set index_path = ''
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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19 #if str($reference_genome.source) == "history":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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20 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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21 ln -s -f '$reference_genome.own_file' genome.fa &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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22 #set index_path = 'genome'
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23 #else:
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iuc
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24 #set index_path = $reference_genome.index.fields.path
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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25 #end if
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27 ## Link in the input files, so bowtie2 can tell their type
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29 #set compressed="False"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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30 #set reads_are_fastq = True
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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parents: 17
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31 #if str($library.type) == 'paired':
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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32 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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33 #set read1 = "input_f.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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34 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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35 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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36 #set read1 = "input_f.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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37 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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38 #else if $library.input_1.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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39 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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40 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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41 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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42 #set read1 = "input_f.fastq"
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43 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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44 ln -f -s '${library.input_1}' ${read1} &&
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45
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46 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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47 #set read2 = "input_r.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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48 #set compressed = "GZ"
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49 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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50 #set read2 = "input_r.fastq.bz2"
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iuc
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51 #set compressed = "BZ2"
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52 #else if $library.input_2.is_of_type('fasta'):
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53 #set read2 = "input_r.fasta"
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54 #else:
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55 #set read2 = "input_r.fastq"
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iuc
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56 #end if
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57 ln -f -s '${library.input_2}' ${read2} &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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58 #else if str($library.type) == 'paired_collection':
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59 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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60 #set read1 = "input_f.fastq.gz"
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61 #set compressed = "GZ"
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iuc
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62 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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63 #set read1 = "input_f.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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64 #set compressed = "BZ2"
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65 #else if $library.input_1.forward.is_of_type('fasta'):
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66 #set reads_are_fastq = False
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iuc
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67 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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68 #else:
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69 #set read1 = "input_f.fastq"
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70 #end if
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71 ln -s '${library.input_1.forward}' ${read1} &&
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72
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73 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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74 #set read2 = "input_r.fastq.gz"
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75 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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76 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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iuc
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77 #set read2 = "input_r.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
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78 #set compressed = "BZ2"
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iuc
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79 #else if $library.input_1.reverse.is_of_type("fasta"):
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iuc
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80 #set read2 = "input_r.fasta"
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81 #else:
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iuc
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82 #set read2 = "input_r.fastq"
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83 #end if
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84 ln -s '${library.input_1.reverse}' ${read2} &&
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85
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86 #else if str($library.type) == 'paired_interleaved':
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87 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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iuc
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diff changeset
88 #set read1 = "input_il.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
89 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
90 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
91 #set read1 = "input_il.fastq.bz2"
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iuc
parents: 17
diff changeset
92 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
93 #else if $library.input_1.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
94 #set reads_are_fastq = False
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iuc
parents: 17
diff changeset
95 #set read1 = "input_il.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
96 #else:
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iuc
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diff changeset
97 #set read1 = "input_il.fastq"
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iuc
parents: 17
diff changeset
98 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
99 ln -s '${library.input_1}' ${read1} &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
100 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
101 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
102 #set read1 = "input_f.fastq.gz"
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iuc
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diff changeset
103 #set compressed = "GZ"
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iuc
parents: 17
diff changeset
104 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
105 #set read1 = "input_f.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
106 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
107 #else if $library.input_1.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff changeset
108 #set reads_are_fastq = False
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iuc
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diff changeset
109 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
110 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
111 #set read1 = "input_f.fastq"
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iuc
parents: 17
diff changeset
112 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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113 ln -s '${library.input_1}' ${read1} &&
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iuc
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diff changeset
114 #end if
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115
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116 ## execute bowtie2
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117
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118 bowtie2
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119
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120 ## number of threads
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121 -p \${GALAXY_SLOTS:-4}
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122
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iuc
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diff changeset
123 ## index file path
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124 -x '$index_path'
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125
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126 ## Input reads are fasta?
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127 #if not reads_are_fastq:
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128 -f
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129 #end if
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130
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131 ## Input reads
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132 #if str( $library.type ) == "single":
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133 -U '${read1}'
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iuc
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diff changeset
134 #if str( $library.unaligned_file ) == "true":
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iuc
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diff changeset
135 #if $compressed == "GZ":
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iuc
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diff changeset
136 --un-gz '${output_unaligned_reads_l}'
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iuc
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diff changeset
137 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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138 --un-bz2 '${output_unaligned_reads_l}'
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
139 #else:
18
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140 --un '${output_unaligned_reads_l}'
14
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141 #end if
18
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diff changeset
142 #end if
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143 #if str( $library.aligned_file ) == "true":
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144 #if $compressed == "GZ":
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iuc
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diff changeset
145 --al-gz '${output_aligned_reads_l}'
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iuc
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diff changeset
146 #else if $compressed == "BZ2":
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iuc
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diff changeset
147 --al-bz2 '${output_aligned_reads_l}'
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148 #else:
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149 --al '${output_aligned_reads_l}'
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
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diff changeset
150 #end if
18
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151 #end if
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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152
18
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153 #elif str( $library.type ) == "paired_interleaved":
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154 --interleaved '${read1}'
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155 #if str( $library.unaligned_file ) == "true":
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iuc
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diff changeset
156 #if $compressed == "GZ":
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iuc
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diff changeset
157 --un-gz '${output_unaligned_reads_l}'
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iuc
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158 #else if $compressed == "BZ2":
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iuc
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diff changeset
159 --un-bz2 '${output_unaligned_reads_l}'
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diff changeset
160 #else:
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iuc
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diff changeset
161 --un '${output_unaligned_reads_l}'
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iuc
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diff changeset
162 #end if
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iuc
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diff changeset
163 #end if
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diff changeset
164 #if str( $library.aligned_file ) == "true":
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iuc
parents: 17
diff changeset
165 #if $compressed == "GZ":
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iuc
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diff changeset
166 --al-gz '${output_aligned_reads_l}'
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iuc
parents: 17
diff changeset
167 #else if $compressed == "BZ2":
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iuc
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diff changeset
168 --al-bz2 '${output_aligned_reads_l}'
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iuc
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diff changeset
169 #else:
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iuc
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diff changeset
170 --al '${output_aligned_reads_l}'
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iuc
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diff changeset
171 #end if
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iuc
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diff changeset
172 #end if
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iuc
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diff changeset
173 #else:
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174 -1 '${read1}'
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diff changeset
175 -2 '${read2}'
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iuc
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diff changeset
176 #if str( $library.unaligned_file ) == "true":
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iuc
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diff changeset
177 #if $compressed == "GZ":
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178 --un-conc-gz '${output_unaligned_reads_l}'
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179 #else if $compressed == "BZ2":
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180 --un-conc-bz2 '${output_unaligned_reads_l}'
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181 #else:
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182 --un-conc '${output_unaligned_reads_l}'
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183 #end if
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184 #end if
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185 #if str( $library.aligned_file ) == "true":
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186 #if $compressed == "GZ":
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187 --al-conc-gz '${output_aligned_reads_l}'
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188 #else if $compressed == "BZ2":
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189 --al-conc-bz2 '${output_aligned_reads_l}'
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190 #else:
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191 --al-conc '${output_aligned_reads_l}'
0
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192 #end if
18
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193 #end if
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194 #if str( $library.paired_options.paired_options_selector ) == "yes":
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195 -I ${library.paired_options.I}
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196 -X ${library.paired_options.X}
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197 ${library.paired_options.fr_rf_ff}
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198 ${library.paired_options.no_mixed}
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199 ${library.paired_options.no_discordant}
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200 ${library.paired_options.dovetail}
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201 ${library.paired_options.no_contain}
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202 ${library.paired_options.no_overlap}
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203 #end if
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204 #end if
7
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205
18
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206 ## Read group information.
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207 @define_read_group_helpers@
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208 #if str( $library.type ) == "single":
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209 #set $rg_auto_name = $read_group_name_default($library.input_1)
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210 #elif str( $library.type ) == "paired":
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211 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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212 #else
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213 #set $rg_auto_name = $read_group_name_default($library.input_1)
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214 #end if
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215 @set_use_rg_var@
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216 @set_read_group_vars@
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217 #if $use_rg
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218 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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219 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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220 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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221 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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222 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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223 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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224 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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225 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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226 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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227 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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228 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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229 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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230 #end if
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231
18
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232 ## Analysis type
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233 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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234 $analysis_type.presets
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235 #elif str( $analysis_type.analysis_type_selector ) == "full":
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236 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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237 --skip ${analysis_type.input_options.skip}
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238 --qupto ${analysis_type.input_options.qupto}
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239 --trim5 ${analysis_type.input_options.trim5}
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240 --trim3 ${analysis_type.input_options.trim3}
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241 ${analysis_type.input_options.qv_encoding}
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242 ${analysis_type.input_options.solexa_quals}
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243 ${analysis_type.input_options.int_quals}
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244 #end if
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245
18
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246 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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247 -N ${analysis_type.alignment_options.N}
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248 -L ${analysis_type.alignment_options.L}
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249 -i '${analysis_type.alignment_options.i}'
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250 --n-ceil '${analysis_type.alignment_options.n_ceil}'
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251 --dpad ${analysis_type.alignment_options.dpad}
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252 --gbar ${analysis_type.alignment_options.gbar}
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253 ${analysis_type.alignment_options.ignore_quals}
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254 ${analysis_type.alignment_options.nofw}
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255 ${analysis_type.alignment_options.norc}
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256 ${analysis_type.alignment_options.no_1mm_upfront}
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257 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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258 --end-to-end
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259 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
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260 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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261 --local
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262 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
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263 #end if
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264 #end if
7
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265
18
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266 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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267 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
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268 --ma ${analysis_type.scoring_options.ma}
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269 #end if
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270 --mp '${analysis_type.scoring_options.mp}'
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271 --np ${analysis_type.scoring_options.np}
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272 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
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273 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
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274 #end if
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275
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276 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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277 -k ${analysis_type.reporting_options.k}
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278 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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279 -a
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280 #end if
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281
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282 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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283 -D ${analysis_type.effort_options.D}
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284 -R ${analysis_type.effort_options.R}
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285 #end if
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286 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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287 ${analysis_type.other_options.non_deterministic}
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288 --seed ${analysis_type.other_options.seed}
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289 #end if
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290
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291 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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292 ${analysis_type.cline}
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293 #end if
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294
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295 #if str( $sam_options.sam_options_selector ) == "yes":
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296 ${sam_options.no_unal}
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297 ${sam_options.omit_sec_seq}
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298 ${sam_options.sam_no_qname_trunc}
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299 ${sam_options.xeq}
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300 ${sam_options.soft_clipped_unmapped_tlen}
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301 ${sam_options.reorder}
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302 #end if
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303
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304 ## mapping stats (i.e. stderr from bowtie2)
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305 #if $save_mapping_stats
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306 2> '$mapping_stats'
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307 #end if
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308
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309 ## output file
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310 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
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311 | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
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312 #else if $sam_options.reorder:
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313 | samtools view --no-PG -bS - -o '$output'
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314 #else:
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315 > '$output'
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316 #end if
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317
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318 ## rename unaligned sequence files
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319 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_unaligned_reads_l and $output_unaligned_reads_r:
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320 #from os.path import splitext
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321 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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322 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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323 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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324 #end if
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325 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_aligned_reads_l and $output_aligned_reads_r:
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326 #from os.path import splitext
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327 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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328 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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329 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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330 #end if
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331
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332 ]]></command>
0
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333 <inputs>
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334 <!-- single/paired -->
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335 <conditional name="library">
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336 <param name="type" type="select" label="Is this single or paired library">
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337 <option value="single">Single-end</option>
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338 <option value="paired">Paired-end</option>
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339 <option value="paired_collection">Paired-end Dataset Collection</option>
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340 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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341 </param>
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342
0
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343 <when value="single">
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344 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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345 <expand macro="align_unalign" />
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346 </when>
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347 <when value="paired">
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348 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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349 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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350 <expand macro="align_unalign" />
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351 <expand macro="paired_end_options" />
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352 </when>
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353 <when value="paired_collection">
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354 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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355 <expand macro="align_unalign" />
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356 <expand macro="paired_end_options" />
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357 </when>
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358 <when value="paired_interleaved">
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359 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
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360 <expand macro="align_unalign" />
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361 <expand macro="paired_end_options" />
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362 </when>
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363 </conditional>
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364 <!-- reference genome -->
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365 <conditional name="reference_genome">
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366 <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">
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367 <option value="indexed">Use a built-in genome index</option>
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368 <option value="history">Use a genome from the history and build index</option>
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369 </param>
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370 <when value="indexed">
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371 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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372 <options from_data_table="bowtie2_indexes">
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373 <filter type="sort_by" column="2"/>
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374 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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375 </options>
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376 </param>
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377 </when>
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378 <when value="history">
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379 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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380 </when>
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381 </conditional>
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382 <!-- read group settings -->
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383 <expand macro="read_group_conditional" />
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384 <conditional name="analysis_type">
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385 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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386 <option value="simple">1: Default setting only</option>
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387 <option value="full">2: Full parameter list</option>
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388 </param>
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389 <when value="simple">
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390 <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.">
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391 <option value="no_presets" selected="True">No, just use defaults</option>
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392 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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393 <option value="--fast">Fast end-to-end (--fast)</option>
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394 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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395 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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396 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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397 <option value="--fast-local">Fast local (--fast-local)</option>
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398 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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399 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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400 </param>
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401 </when>
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402 <when value="full">
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403 <conditional name="input_options">
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404 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See &quot;Input Options&quot; section of Help below for information">
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405 <option value="yes">Yes</option>
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406 <option value="no" selected="true">No</option>
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407 </param>
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408 <when value="yes">
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409 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/>
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410 <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"/>
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411 <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"/>
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412 <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"/>
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413 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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414 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>
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415 <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>
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416 </param>
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417 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/>
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418 <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"/>
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419 </when>
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420 <when value="no">
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421 <!-- do nothing -->
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422 </when>
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423 </conditional>
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424 <conditional name="alignment_options">
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425 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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426 <option value="yes">Yes</option>
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427 <option value="no" selected="true">No</option>
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428 </param>
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429 <when value="yes">
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430 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
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431 <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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432 <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
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433 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
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434 <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"/>
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435 <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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436 <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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437 <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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438 <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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439 <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"/>
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440 <conditional name="align_mode">
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441 <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">
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442 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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443 <option value="local">Local (--local)</option>
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444 </param>
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445 <when value="end-to-end">
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446 <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`"/>
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447 </when>
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448 <when value="local">
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449 <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`"/>
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450 </when>
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451 </conditional>
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452 </when>
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453 <when value="no">
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454 <!-- do nothing -->
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455 </when>
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456 </conditional>
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457 <conditional name="scoring_options">
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458 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See &quot;Scoring Options&quot; section of Help below for information">
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459 <option value="yes">Yes</option>
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460 <option value="no" selected="true">No</option>
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461 </param>
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462 <when value="yes">
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463 <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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464 <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"/>
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465 <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"/>
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466 <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"/>
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467 <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"/>
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468 <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"/>
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469 <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"/>
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470 </when>
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471 <when value="no">
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472 <!-- do nothing -->
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473 </when>
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474 </conditional>
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475 <conditional name="reporting_options">
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476 <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 &quot;Reporting Options&quot; section of Help below for information on -k and -a options">
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477 <option value="no" selected="true">No, do not set</option>
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478 <option value="k">Set -k option and enter -k value</option>
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479 <option value="a">Set -a option</option>
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480 </param>
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481 <when value="no">
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482 <!-- do nothing -->
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parents: 0
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483 </when>
3
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parents: 2
diff changeset
484 <when value="k">
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parents: 2
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485 <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
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parents: 0
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486 </when>
3
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parents: 2
diff changeset
487 <when value="a">
2
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parents: 0
diff changeset
488 <!-- do nothing here; set -a flag on the command line-->
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parents: 0
diff changeset
489 </when>
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parents: 0
diff changeset
490 </conditional>
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parents: 0
diff changeset
491 <conditional name="effort_options">
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parents: 0
diff changeset
492 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See &quot;Effort Options&quot; section of Help below for information">
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parents: 0
diff changeset
493 <option value="yes">Yes</option>
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parents: 0
diff changeset
494 <option value="no" selected="true">No</option>
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devteam
parents: 0
diff changeset
495 </param>
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parents: 0
diff changeset
496 <when value="yes">
3
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parents: 2
diff changeset
497 <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
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parents: 0
diff changeset
498 <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"/>
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parents: 0
diff changeset
499 </when>
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parents: 0
diff changeset
500 <when value="no">
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parents: 0
diff changeset
501 <!-- do nothing -->
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parents: 0
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502 </when>
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diff changeset
503 </conditional>
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parents: 0
diff changeset
504 <conditional name="other_options">
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parents: 0
diff changeset
505 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
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parents: 0
diff changeset
506 <option value="yes">Yes</option>
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parents: 0
diff changeset
507 <option value="no" selected="true">No</option>
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parents: 0
diff changeset
508 </param>
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parents: 0
diff changeset
509 <when value="yes">
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parents: 0
diff changeset
510 <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
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parents: 2
diff changeset
511 <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
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
512 </when>
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parents: 0
diff changeset
513 <when value="no">
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parents: 0
diff changeset
514 <!-- do nothing -->
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parents: 0
diff changeset
515 </when>
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parents: 0
diff changeset
516 </conditional>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
517 </when>
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parents: 21
diff changeset
518 </conditional>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
519 <conditional name="sam_options">
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iuc
parents: 21
diff changeset
520 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
521 <option value="yes">Yes</option>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
522 <option value="no" selected="true">No</option>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
523 </param>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
524 <when value="yes">
7
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parents: 6
diff changeset
525 <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."/>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
526 <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"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
527 <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"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
528 <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
529 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
530 <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
531 <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
532 label="Reorder output to reflect order of the input file"
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
533 help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
534 </when>
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
535 <when value="no"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
536 </conditional>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
537 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
538 </inputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
539 <!-- define outputs -->
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
540 <outputs>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
541 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
2
c1ec08cb34f9 Uploaded
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parents: 0
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542 <filter>library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
543 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
544 <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
545 <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
546 <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
547 <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
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parents: 6
diff changeset
548 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
549 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
550 <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
551 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
552 <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
553 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
554 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
555 <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
556 <action type="format">
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parents: 6
diff changeset
557 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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parents: 6
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558 </action>
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parents: 6
diff changeset
559 </when>
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parents: 6
diff changeset
560 </conditional>
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iuc
parents: 22
diff changeset
561 <expand macro="dbKeyActions" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
562 </actions>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
563 </data>
10
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parents: 8
diff changeset
564 <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
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diff changeset
565 <filter>library['aligned_file'] 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: 8
diff changeset
566 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
567 <conditional name="library.type">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
568 <when value="single">
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parents: 8
diff changeset
569 <action type="format">
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parents: 8
diff changeset
570 <option type="from_param" name="library.input_1" param_attribute="ext" />
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parents: 8
diff changeset
571 </action>
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diff changeset
572 </when>
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parents: 8
diff changeset
573 <when value="paired">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
574 <action type="format">
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parents: 8
diff changeset
575 <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
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parents: 8
diff changeset
576 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
577 </when>
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parents: 8
diff changeset
578 <when value="paired_collection">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
579 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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diff changeset
580 <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
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parents: 8
diff changeset
581 </action>
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parents: 8
diff changeset
582 </when>
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parents: 8
diff changeset
583 </conditional>
23
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iuc
parents: 22
diff changeset
584 <expand macro="dbKeyActions" />
10
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parents: 8
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585 </actions>
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parents: 8
diff changeset
586 </data>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
587 <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
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parents: 8
diff changeset
588 <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
589 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
590 <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
591 <when value="paired">
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devteam
parents: 8
diff changeset
592 <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
593 <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
594 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
595 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
596 <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
597 <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
598 <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
599 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
600 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
601 </conditional>
23
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iuc
parents: 22
diff changeset
602 <expand macro="dbKeyActions" />
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
603 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
604 </data>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
605 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
606 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
607 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
608 <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
609 <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
610 <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
611 <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
612 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
613 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
614 <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
615 <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
616 <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
617 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
618 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
619 </conditional>
23
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iuc
parents: 22
diff changeset
620 <expand macro="dbKeyActions" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
621 </actions>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
622 </data>
24
017aba02828d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
623 <data format="bam" name="output" label="${tool.name} on ${on_string}: alignments">
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
624 <change_format>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
625 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
24
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iuc
parents: 23
diff changeset
626 <when input="sam_options.sam_opt" value="true" format="sam" />
22
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
627 </change_format>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
628 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
629 <conditional name="reference_genome.source">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
630 <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
631 <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
632 <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: 6
diff changeset
633 <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
devteam
parents: 6
diff changeset
634 <filter type="param_value" ref="reference_genome.index" column="0"/>
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parents: 6
diff changeset
635 </option>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
636 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
637 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
638 <when value="history">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
639 <action type="metadata" name="dbkey">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
640 <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: 6
diff changeset
641 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
642 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
643 </conditional>
23
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iuc
parents: 22
diff changeset
644 <expand macro="dbKeyActions" />
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
645 </actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
646 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
647 <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
devteam
parents: 8
diff changeset
648 <filter>save_mapping_stats is True</filter>
23
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iuc
parents: 22
diff changeset
649 <actions>
17062a0decb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents: 22
diff changeset
650 <expand macro="dbKeyActions" />
17062a0decb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents: 22
diff changeset
651 </actions>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
652 </data>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
653 </outputs>
96d2e31a3938 Imported from capsule None
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diff changeset
654 <tests>
24
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iuc
parents: 23
diff changeset
655 <test expect_num_outputs="1">
17
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diff changeset
656 <!-- test on paired-end datasets -->
2
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devteam
parents: 0
diff changeset
657 <param name="type" value="paired"/>
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parents: 0
diff changeset
658 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
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diff changeset
659 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
660 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
661 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
662 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
663 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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devteam
parents: 0
diff changeset
664 <param name="own_file" value="bowtie2-ref.fasta" />
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iuc
parents: 28
diff changeset
665 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
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666 <metadata name="sort_order" value="coordinate"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
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667 </output>
0
96d2e31a3938 Imported from capsule None
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668 </test>
25
749c918495f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit be3590f33762e4797eaa1462d495e8e8a1b98110"
iuc
parents: 24
diff changeset
669 <test expect_num_outputs="3">
749c918495f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit be3590f33762e4797eaa1462d495e8e8a1b98110"
iuc
parents: 24
diff changeset
670 <!-- test on list paired collection -->
17
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iuc
parents: 16
diff changeset
671 <param name="type" value="paired_collection"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
672 <param name="paired_options_selector" value="no"/>
25
749c918495f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit be3590f33762e4797eaa1462d495e8e8a1b98110"
iuc
parents: 24
diff changeset
673 <param name="unaligned_file" value="true"/>
17
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iuc
parents: 16
diff changeset
674 <param name="analysis_type_selector" value="simple"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
675 <param name="source" value="history" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
676 <param name="input_1">
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
677 <collection type="paired">
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
678 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
679 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
680 </collection>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
681 </param>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
682 <param name="own_file" value="bowtie2-ref.fasta" />
29
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iuc
parents: 28
diff changeset
683 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
684 <metadata name="sort_order" value="coordinate"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
685 </output>
17
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iuc
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diff changeset
686 </test>
24
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iuc
parents: 23
diff changeset
687 <test expect_num_outputs="1">
17
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iuc
parents: 16
diff changeset
688 <!-- test on paired-end datasets with read group info -->
5
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devteam
parents: 4
diff changeset
689 <param name="type" value="paired"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
690 <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
devteam
parents: 4
diff changeset
691 <param name="unaligned_file" value="false"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
692 <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: 4
diff changeset
693 <param name="rg_selector" value="set"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
694 <param name="ID" value="rg1"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
695 <param name="PL" value="CAPILLARY"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
696 <param name="source" value="history" />
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
697 <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
devteam
parents: 4
diff changeset
698 <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
devteam
parents: 4
diff changeset
699 <param name="own_file" value="bowtie2-ref.fasta" />
29
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
700 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4" sort="true">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
701 <metadata name="sort_order" value="coordinate"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
702 </output>
5
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devteam
parents: 4
diff changeset
703 </test>
24
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iuc
parents: 23
diff changeset
704 <test expect_num_outputs="2">
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
705 <!-- test on paired-end datasets with stats output -->
10
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devteam
parents: 8
diff changeset
706 <param name="type" value="paired"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
707 <param name="paired_options_selector" value="no"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
708 <param name="unaligned_file" value="false"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
709 <param name="analysis_type_selector" value="simple"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
710 <param name="source" value="history" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
711 <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
devteam
parents: 8
diff changeset
712 <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
devteam
parents: 8
diff changeset
713 <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
devteam
parents: 8
diff changeset
714 <param name="save_mapping_stats" value="true" />
29
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
715 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
716 <metadata name="sort_order" value="coordinate"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
717 </output>
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
718 <output name="mapping_stats">
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
719 <assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
720 <has_text text="of these" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
721 </assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
722 </output>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
723 </test>
24
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iuc
parents: 23
diff changeset
724 <test expect_num_outputs="1">
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
725 <!-- test on interleaved dataset -->
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
726 <param name="type" value="paired_interleaved"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
727 <!-- <param name="paired_options_selector" value="no"/> -->
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
728 <param name="unaligned_file" value="false"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
729 <param name="analysis_type_selector" value="simple"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
730 <param name="rg_selector" value="set"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
731 <param name="ID" value="rg1"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
732 <param name="PL" value="CAPILLARY"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
733 <param name="source" value="history" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
734 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
735 <param name="own_file" value="bowtie2-ref.fasta" />
29
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
736 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4" sort="true">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
737 <metadata name="sort_order" value="coordinate"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
738 </output>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
739 </test>
24
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iuc
parents: 23
diff changeset
740 <test expect_num_outputs="1">
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
741 <!-- test on fastqsanger.gz paired-end datasets -->
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
742 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
743 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
744 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
745 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
746 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
747 <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
devteam
parents: 13
diff changeset
748 <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
devteam
parents: 13
diff changeset
749 <param name="own_file" value="bowtie2-ref.fasta" />
29
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
750 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
751 <metadata name="sort_order" value="coordinate"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
752 </output>
14
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devteam
parents: 13
diff changeset
753 </test>
24
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iuc
parents: 23
diff changeset
754 <test expect_num_outputs="1">
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
755 <!-- test on fastqsanger.bz2 paired-end datasets -->
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
756 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
757 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
758 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
759 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
760 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
761 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
762 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
763 <param name="own_file" value="bowtie2-ref.fasta" />
29
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
764 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
765 <metadata name="sort_order" value="coordinate"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
766 </output>
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
767 </test>
24
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iuc
parents: 23
diff changeset
768 <test expect_num_outputs="1">
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
769 <!-- test on fasta paired-end datasets -->
16
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parents: 15
diff changeset
770 <param name="type" value="paired"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
771 <param name="paired_options_selector" value="no"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
772 <param name="unaligned_file" value="false"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
773 <param name="analysis_type_selector" value="simple"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
774 <param name="source" value="history" />
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
775 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
776 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
777 <param name="own_file" value="bowtie2-ref.fasta" />
29
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parents: 28
diff changeset
778 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4" sort="true">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
779 <metadata name="sort_order" value="coordinate"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents: 28
diff changeset
780 </output>
16
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diff changeset
781 </test>
24
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iuc
parents: 23
diff changeset
782 <test expect_num_outputs="1">
22
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iuc
parents: 21
diff changeset
783 <!-- test on fasta paired-end datasets with bam_native as output -->
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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parents: 21
diff changeset
784 <param name="type" value="paired"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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parents: 21
diff changeset
785 <param name="paired_options_selector" value="no"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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diff changeset
786 <param name="unaligned_file" value="false"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
787 <param name="analysis_type_selector" value="simple"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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diff changeset
788 <param name="source" value="history" />
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
789 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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diff changeset
790 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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diff changeset
791 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
792 <param name="sam_options_selector" value="yes" />
c3dd1aeb7d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
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diff changeset
793 <param name="reorder" value="true" />
29
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diff changeset
794 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" lines_diff="4">
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
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diff changeset
795 <metadata name="sort_order" value="unsorted"/>
f6877ad76b00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
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diff changeset
796 </output>
22
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diff changeset
797 </test>
24
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parents: 23
diff changeset
798 <test expect_num_outputs="1">
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diff changeset
799 <!-- test on fasta paired-end datasets with sam as output -->
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iuc
parents: 23
diff changeset
800 <param name="type" value="paired"/>
017aba02828d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
801 <param name="paired_options_selector" value="no"/>
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parents: 23
diff changeset
802 <param name="unaligned_file" value="false"/>
017aba02828d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
803 <param name="analysis_type_selector" value="simple"/>
017aba02828d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
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parents: 23
diff changeset
804 <param name="source" value="history" />
017aba02828d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents: 23
diff changeset
805 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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iuc
parents: 23
diff changeset
806 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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parents: 23
diff changeset
807 <param name="own_file" value="bowtie2-ref.fasta" />
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parents: 23
diff changeset
808 <param name="sam_options_selector" value="yes" />
017aba02828d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
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parents: 23
diff changeset
809 <param name="sam_options|sam_opt" value="true" />
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diff changeset
810 <output name="output" ftype="sam">
29
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diff changeset
811 <metadata name="sort_order" value="unsorted"/>
24
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parents: 23
diff changeset
812 <assert_contents>
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parents: 23
diff changeset
813 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
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diff changeset
814 </assert_contents>
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diff changeset
815 </output>
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816 </test>
0
96d2e31a3938 Imported from capsule None
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diff changeset
817 </tests>
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818 <help><![CDATA[
0
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819 **Bowtie2 Overview**
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820
2
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821 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.
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822 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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823
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824 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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825 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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826 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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827
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828 -----
0
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829
2
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830 **Selecting reference genomes for Bowtie2**
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831
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832 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
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833
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834 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
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835 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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836
2
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diff changeset
837 If your genome of interest is not listed here you have two choices:
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838
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839 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
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840 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
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841
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842 ------
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843
2
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diff changeset
844 .. class:: infomark
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845
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diff changeset
846 **Bowtie2 options**
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847
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diff changeset
848 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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849
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850 -----
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851
0
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852 **Inputs**
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853
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diff changeset
854 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section).
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855
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856 ------
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857
2
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858 **Input options**::
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859
15
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parents: 14
diff changeset
860 --interleaved
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861 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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862
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863 -s/--skip <int>
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864 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
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865
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866 -u/--qupto <int>
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867 Align the first `<int>` reads or read pairs from the input (after the
2
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868 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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869
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870 -5/--trim5 <int>
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871 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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872
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873 -3/--trim3 <int>
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874 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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875
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diff changeset
876 --phred33
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diff changeset
877 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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diff changeset
878 also called the "Phred+33" encoding, which is used by the very latest Illumina
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diff changeset
879 pipelines.
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diff changeset
880
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diff changeset
881 --phred64
3
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diff changeset
882 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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diff changeset
883 also called the "Phred+64" encoding.
0
96d2e31a3938 Imported from capsule None
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884
2
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diff changeset
885 --solexa-quals
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diff changeset
886 Convert input qualities from Solexa Phred quality (which can be negative) to
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diff changeset
887 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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diff changeset
888 Pipeline versions (prior to 1.3). Default: off.
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diff changeset
889
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parents: 0
diff changeset
890 --int-quals
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diff changeset
891 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
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diff changeset
892 Integers are treated as being on the Phred quality scale unless
2
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diff changeset
893 `--solexa-quals` is also specified. Default: off.
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894
2
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parents: 0
diff changeset
895 ------
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896
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897 **Presets in `--end-to-end` mode**::
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parents: 0
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898
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parents: 0
diff changeset
899 --very-fast
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parents: 0
diff changeset
900 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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parents: 0
diff changeset
901
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diff changeset
902 --fast
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parents: 0
diff changeset
903 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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parents: 10
diff changeset
904
2
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905 --sensitive
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diff changeset
906 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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907
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908 --very-sensitive
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909 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
96d2e31a3938 Imported from capsule None
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910
96d2e31a3938 Imported from capsule None
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911 ------
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912
2
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913 **Presets options in `--local` mode**::
0
96d2e31a3938 Imported from capsule None
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914
2
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915 --very-fast-local
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diff changeset
916 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
96d2e31a3938 Imported from capsule None
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917
2
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918 --fast-local
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diff changeset
919 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
96d2e31a3938 Imported from capsule None
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920
2
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921 --sensitive-local
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922 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
96d2e31a3938 Imported from capsule None
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923
2
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924 --very-sensitive-local
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diff changeset
925 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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926
0
96d2e31a3938 Imported from capsule None
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parents:
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927 ------
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928
2
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929 **Alignment options**::
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diff changeset
930
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diff changeset
931 -N <int>
3
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932 Sets the number of mismatches to allowed in a seed alignment during multiseed
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diff changeset
933 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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934 (often much slower) but increases sensitivity. Default: 0.
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935
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diff changeset
936 -L <int>
3
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937 Sets the length of the seed substrings to align during multiseed alignment.
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938 Smaller values make alignment slower but more sensitive. Default: the
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939 `--sensitive` preset is used by default, which sets `-L` to 22 in
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940 `--end-to-end` mode and to 20 in `--local` mode.
2
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941
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diff changeset
942 -i <func>
2
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943 Sets a function governing the interval between seed substrings to use during
3
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944 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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945 length is 10, and the seed interval is 6, the seeds extracted will be:
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946
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947 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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948 Seed 1 fw: TAGCTACGCT
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949 Seed 1 rc: AGCGTAGCTA
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950 Seed 2 fw: CGCTCTACGC
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951 Seed 2 rc: GCGTAGAGCG
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952 Seed 3 fw: ACGCTATCAT
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953 Seed 3 rc: ATGATAGCGT
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954 Seed 4 fw: TCATGCATAA
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955 Seed 4 rc: TTATGCATGA
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956
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957 Since it's best to use longer intervals for longer reads, this parameter sets
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958 the interval as a function of the read length, rather than a single
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959 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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960 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
3
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961 If the function returns a result less than
2
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962 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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963 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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964 in `--local` mode.
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965
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966 --n-ceil <func>
2
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967 Sets a function governing the maximum number of ambiguous characters (usually
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968 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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969 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
3
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970 where x is the read length. Reads exceeding this ceiling are filtered out.
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971 Default: `L,0,0.15`.
2
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972
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973 --dpad <int>
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974 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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975 gaps. Default: 15.
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976
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977 --gbar <int>
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978 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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979 Default: 4.
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980
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981 --ignore-quals
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982 When calculating a mismatch penalty, always consider the quality value at the
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983 mismatched position to be the highest possible, regardless of the actual value.
2
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984 I.e. input is treated as though all quality values are high. This is also the
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985 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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986 `-r`, or `-c` modes).
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987
2
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988 --nofw/--norc
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989 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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990 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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991 not attempt to align unpaired reads against the reverse-complement (Crick)
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992 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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993 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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994 paired-end configurations corresponding to fragments from the reverse-complement
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995 (Crick) strand. Default: both strands enabled.
2
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996
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997 --no-1mm-upfront
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998 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
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999 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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1000 alignments can be found very quickly, and many short read alignments have exact or
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1001 near-exact end-to-end alignments. However, this can lead to unexpected
3
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1002 alignments when the user also sets options governing the multiseed heuristic,
2
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1003 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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1004 to the length of the read, the user will be surprised to find 1-mismatch alignments
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1005 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
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1006 alignments before using the multiseed heuristic, which leads to the expected
2
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1007 behavior when combined with options such as `-L` and `-N`. This comes at the
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1008 expense of speed.
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1009
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1010 --end-to-end
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1011 In this mode, Bowtie 2 requires that the entire read align from one end to the
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1012 other, without any trimming (or "soft clipping") of characters from either end.
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1013 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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1014 are less than or equal to 0, and the greatest possible alignment score is 0.
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1015 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
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1016
2
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1017 --local
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1018 In this mode, Bowtie 2 does not require that the entire read align from one end
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1019 to the other. Rather, some characters may be omitted ("soft clipped") from the
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1020 ends in order to achieve the greatest possible alignment score. The match bonus
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1021 `--ma` is used in this mode, and the best possible alignment score is equal to
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1022 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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1023 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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1024 the local version of the preset (`--very-fast-local`). This is mutually
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1025 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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1026
2
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1027 -----
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1028
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1029 **Scoring options**::
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1030
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1031 --ma <int>
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1032 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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1033 score for each position where a read character aligns to a reference character
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1034 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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1035
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1036 --mp MX,MN
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1037 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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1038 number less than or equal to `MX` and greater than or equal to `MN` is
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1039 subtracted from the alignment score for each position where a read character
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1040 aligns to a reference character, the characters do not match, and neither is an
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1041 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1042 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1043 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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1044
11
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diff changeset
1045 --np <int>
2
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diff changeset
1046 Sets penalty for positions where the read, reference, or both, contain an
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diff changeset
1047 ambiguous character such as `N`. Default: 1.
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diff changeset
1048
11
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diff changeset
1049 --rdg <int1>,<int2>
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diff changeset
1050 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1051 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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diff changeset
1052
11
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diff changeset
1053 --rfg <int1>,<int2>
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diff changeset
1054 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1055 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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diff changeset
1056 5, 3.
0
96d2e31a3938 Imported from capsule None
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1057
11
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diff changeset
1058 --score-min <func>
2
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1059 Sets a function governing the minimum alignment score needed for an alignment to
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1060 be considered "valid" (i.e. good enough to report). This is a function of read
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1061 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
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1062 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
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1063 the default in `--local` mode is `G,20,8`.
11
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1064
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1065 -----
2
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1066
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1067 **Reporting options**::
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1068
11
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1069 -k <int>
2
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1070 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1071 When it finds a valid alignment, it continues looking for alignments that are
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1072 nearly as good or better. The best alignment found is reported (randomly
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1073 selected from among best if tied). Information about the best alignments is
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1074 used to estimate mapping quality and to set SAM optional fields, such as
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1075 `AS:i` and `XS:i`.
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1076
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1077 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
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1078 searches for at most `<int>` distinct, valid alignments for each read. The
2
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1079 search terminates when it can't find more distinct valid alignments, or when it
11
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1080 finds `<int>`, whichever happens first. All alignments found are reported in
2
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1081 descending order by alignment score. The alignment score for a paired-end
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1082 alignment equals the sum of the alignment scores of the individual mates. Each
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1083 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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1084 (which equals 256) set in its FLAGS field. For reads that have more than
11
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diff changeset
1085 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
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1086 `<int>` alignments reported are the best possible in terms of alignment score.
2
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1087 `-k` is mutually exclusive with `-a`.
0
96d2e31a3938 Imported from capsule None
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1088
2
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1089 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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1090 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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1091
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1092 -a
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1093 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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1094 is mutually exclusive with `-k`.
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1095
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1096 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
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diff changeset
1097 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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1098
2
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1099 -----
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1100
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1101 **Effort options**::
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1102
11
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1103 -D <int>
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1104 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1105 moves on, using the alignments found so far. A seed extension "fails" if it
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1106 does not yield a new best or a new second-best alignment. This limit is
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1107 automatically adjusted up when -k or -a are specified. Default: 15.
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1108
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1109 -R <int>
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1110 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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1111 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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1112 (same length, same number of mismatches allowed) at different offsets and
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1113 searches for more alignments. A read is considered to have repetitive seeds if
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1114 the total number of seed hits divided by the number of seeds that aligned at
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1115 least once is greater than 300. Default: 2.
11
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1116
2
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1117 -----
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1118
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1119 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
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1120
11
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1121 -I/--minins <int>
2
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1122 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
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1123 specified and a paired-end alignment consists of two 20-bp alignments in the
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1124 appropriate orientation with a 20-bp gap between them, that alignment is
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1125 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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1126 be valid in that case. If trimming options `-3` or `-5` are also used, the
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1127 `-I` constraint is applied with respect to the untrimmed mates.
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1128
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1129 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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1130 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1131 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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1132 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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1133 efficient.
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1134
11
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1135 Default: 0 (essentially imposing no minimum)
2
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1136
11
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1137 -X/--maxins <int>
2
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1138 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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1139 is specified and a paired-end alignment consists of two 20-bp alignments in the
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1140 proper orientation with a 60-bp gap between them, that alignment is considered
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1141 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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1142 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1143 constraint is applied with respect to the untrimmed mates, not the trimmed
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1144 mates.
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1145
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1146 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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1147 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1148 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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diff changeset
1149 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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1150 efficient.
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1151
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1152 Default: 500.
0
96d2e31a3938 Imported from capsule None
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1153
2
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1154 --fr/--rf/--ff
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1155 The upstream/downstream mate orientations for a valid paired-end alignment
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1156 against the forward reference strand. E.g., if `--fr` is specified and there is
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1157 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1158 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1159 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1160 complement of mate 1 and all other constraints are met, that too is valid.
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1161 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1162 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1163 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1164 for Illumina's Paired-end Sequencing Assay).
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1165
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1166 --no-mixed
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1167 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1168 a pair, it then tries to find alignments for the individual mates. This option
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1169 disables that behavior.
0
96d2e31a3938 Imported from capsule None
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1170
2
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1171 --no-discordant
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1172 By default, `bowtie2` looks for discordant alignments if it cannot find any
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1173 concordant alignments. A discordant alignment is an alignment where both mates
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1174 align uniquely, but that does not satisfy the paired-end constraints
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1175 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1176
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1177 --dovetail
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1178 If the mates "dovetail", that is if one mate alignment extends past the
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1179 beginning of the other such that the wrong mate begins upstream, consider that
3
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1180 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1181
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1182 --no-contain
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1183 If one mate alignment contains the other, consider that to be non-concordant.
3
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1184 Default: a mate can contain the other in a concordant alignment.
2
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1185
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1186 --no-overlap
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1187 If one mate alignment overlaps the other at all, consider that to be
3
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1188 non-concordant. Default: mates can overlap in a concordant alignment.
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1189
0
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1190 ------
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1191
2
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1192 **SAM options**::
0
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1193
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1194 --rg-id <text>
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1195 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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1196 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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1197 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1198 value set to `<text>`.
0
96d2e31a3938 Imported from capsule None
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diff changeset
1199
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1200 --rg <text>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1201 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
c1ec08cb34f9 Uploaded
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diff changeset
1202 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
ceb6467e276c Uploaded
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diff changeset
1203 must also be specified. This is because the `ID` tag is required by the SAM
ceb6467e276c Uploaded
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diff changeset
1204 Specification. Specify `--rg` multiple times to set multiple fields. See the
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diff changeset
1205 SAM Specification for details about what fields are legal.
0
96d2e31a3938 Imported from capsule None
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diff changeset
1206
2
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diff changeset
1207 --omit-sec-seq
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diff changeset
1208 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
c1ec08cb34f9 Uploaded
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diff changeset
1209 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
c1ec08cb34f9 Uploaded
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diff changeset
1210 in those fields instead.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1211
2
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diff changeset
1212 -----
0
96d2e31a3938 Imported from capsule None
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1213
2
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diff changeset
1214 **Other options**::
0
96d2e31a3938 Imported from capsule None
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diff changeset
1215
2
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1216 --reorder
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diff changeset
1217 Guarantees that output SAM records are printed in an order corresponding to the
c1ec08cb34f9 Uploaded
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diff changeset
1218 order of the reads in the original input file, even when `-p` is set greater
c1ec08cb34f9 Uploaded
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diff changeset
1219 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
c1ec08cb34f9 Uploaded
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diff changeset
1220 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
c1ec08cb34f9 Uploaded
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diff changeset
1221 not specified. Has no effect if `-p` is set to 1, since output order will
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1222 naturally correspond to input order in that case.
0
96d2e31a3938 Imported from capsule None
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1223
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1224 --seed <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1225 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
96d2e31a3938 Imported from capsule None
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1226
2
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1227 --non-deterministic
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diff changeset
1228 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
c1ec08cb34f9 Uploaded
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diff changeset
1229 seeds the generator with a number derived from (a) the read name, (b) the
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diff changeset
1230 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1231 option. This means that if two reads are identical (same name, same
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1232 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1233 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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1234 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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diff changeset
1235 current time. This means that Bowtie 2 will not necessarily report the same
c1ec08cb34f9 Uploaded
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diff changeset
1236 alignment for two identical reads. This is counter-intuitive for some users,
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diff changeset
1237 but might be more appropriate in situations where the input consists of many
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diff changeset
1238 identical reads.
0
96d2e31a3938 Imported from capsule None
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1239
15
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1240 -----
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1241
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1242
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diff changeset
1243 **Paired-end (and mate-pair) data in fastq format**
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1244
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diff changeset
1245 Paired end datasets can be represented as two individual datasets:
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1246
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diff changeset
1247 First dataset::
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1248
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1249 @1/1
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1250 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1251 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1252 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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1253 @2/1
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1254 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1255 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1256 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1257
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diff changeset
1258 Second dataset::
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1259
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1260 @1/2
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diff changeset
1261 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1262 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1263 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1264 @2/2
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diff changeset
1265 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1266 +
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1267 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
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1268
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1269 Or a single *interleaved* dataset::
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1270
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1271 @1/1
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1272 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1273 +
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1274 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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1275 @1/2
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1276 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1277 +
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1278 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
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1279 @2/1
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1280 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1281 +
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1282 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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1283 @2/2
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1284 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1285 +
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1286 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1287 ]]></help>
2
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1288 <citations>
17
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diff changeset
1289 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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diff changeset
1290 <citation type="doi">10.1038/nmeth.1923</citation>
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diff changeset
1291 </citations>
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96d2e31a3938 Imported from capsule None
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1292 </tool>