Mercurial > repos > devteam > bowtie2
annotate bowtie2_wrapper.xml @ 33:c3d19e7ee879 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
| author | iuc |
|---|---|
| date | Wed, 24 Sep 2025 13:36:57 +0000 |
| parents | 6b4916819621 |
| children |
| rev | line source |
|---|---|
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33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 | 2 <description>- map reads against reference genome</description> |
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31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
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changeset
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3 <macros> |
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f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
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diff
changeset
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4 <import>bowtie2_macros.xml</import> |
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f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
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changeset
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5 </macros> |
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29
56dcf3929d02
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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changeset
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6 <xrefs> |
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56dcf3929d02
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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changeset
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7 <xref type="bio.tools">bowtie2</xref> |
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56dcf3929d02
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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changeset
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8 </xrefs> |
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fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
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changeset
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9 <requirements> |
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c9105910063f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
iuc
parents:
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changeset
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10 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement> |
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33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
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11 <requirement type="package" version="1.22.1">samtools</requirement> |
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fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
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diff
changeset
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12 </requirements> |
| 0 | 13 <version_command>bowtie2 --version</version_command> |
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fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
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changeset
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14 <command detect_errors="exit_code"><![CDATA[ |
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e798c0b3384c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents:
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changeset
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15 ## Use pipefail if available to quit with first non-zero exit code |
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e798c0b3384c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents:
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changeset
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16 set -o | grep -q pipefail && set -o pipefail; |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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17 ## prepare bowtie2 index |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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18 #set index_path = '' |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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19 #if str($reference_genome.source) == "history": |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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20 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome && |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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21 ln -s -f '$reference_genome.own_file' genome.fa && |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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22 #set index_path = 'genome' |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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23 #else: |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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24 #set index_path = $reference_genome.index.fields.path |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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25 #end if |
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5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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diff
changeset
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26 |
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18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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27 ## Link in the input files, so bowtie2 can tell their type |
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85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
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diff
changeset
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28 |
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18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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29 #set compressed="False" |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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30 #set reads_are_fastq = True |
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33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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31 #if str($library.type) == 'paired_collection': |
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18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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32 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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33 #set read1 = "input_f.fastq.gz" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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34 #set compressed = "GZ" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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35 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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36 #set read1 = "input_f.fastq.bz2" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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37 #set compressed = "BZ2" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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38 #else if $library.input_1.forward.is_of_type('fasta'): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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39 #set reads_are_fastq = False |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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40 #set read1 = "input_f.fasta" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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41 #else: |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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42 #set read1 = "input_f.fastq" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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43 #end if |
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33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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44 ln -f -s '${library.input_1.forward}' ${read1} && |
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85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
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45 |
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18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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46 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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47 #set read2 = "input_r.fastq.gz" |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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48 #set compressed = "GZ" |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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49 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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50 #set read2 = "input_r.fastq.bz2" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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51 #set compressed = "BZ2" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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52 #else if $library.input_1.reverse.is_of_type("fasta"): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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53 #set read2 = "input_r.fasta" |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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54 #else: |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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55 #set read2 = "input_r.fastq" |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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56 #end if |
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33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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57 ln -f -s '${library.input_1.reverse}' ${read2} && |
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18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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58 #else: |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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59 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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60 #set read1 = "input_f.fastq.gz" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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61 #set compressed = "GZ" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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62 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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63 #set read1 = "input_f.fastq.bz2" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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64 #set compressed = "BZ2" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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65 #else if $library.input_1.is_of_type("fasta"): |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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66 #set reads_are_fastq = False |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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67 #set read1 = "input_f.fasta" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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68 #else: |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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69 #set read1 = "input_f.fastq" |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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70 #end if |
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33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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71 ln -f -s '${library.input_1}' ${read1} && |
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18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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72 #end if |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
17
diff
changeset
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73 |
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33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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74 |
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c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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75 ## compute number of threads to be used for bowtie2 |
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c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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76 ## the bowtie parameter -p specifies the number of alignment threads to use (in |
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c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
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77 ## addition to a control thread) # just using GALAXY_SLOTS will lead to |
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c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
78 ## overcommiting ressources (in particular because there may be a samtools sort or view |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
79 ## running in parallel). |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
80 ## for now we use one thread less than GALAXY_SLOTS |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
81 THREADS=\${GALAXY_SLOTS:-4} && |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
82 if [ "\$THREADS" -gt 1 ]; then (( THREADS-- )); fi && |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
83 |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
84 ## execute bowtie2 |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
85 |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
86 bowtie2 |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
87 |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
88 ## number of threads |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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diff
changeset
|
89 -p "\$THREADS" |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
90 |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
91 ## index file path |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
|
92 -x '$index_path' |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
93 |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
94 ## Input reads are fasta? |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
|
95 #if not reads_are_fastq: |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
96 -f |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
|
97 #end if |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
98 |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
99 ## Input reads |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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100 #if str( $library.type ) == "single": |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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101 -U '${read1}' |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
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102 #if str( $library.unaligned_file ) == "true": |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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103 #if $compressed == "GZ": |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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diff
changeset
|
104 --un-gz 'unaligned_reads' |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
|
105 #else if $compressed == "BZ2": |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
106 --un-bz2 'unaligned_reads' |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
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changeset
|
107 #else: |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
108 --un 'unaligned_reads' |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
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changeset
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109 #end if |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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110 #end if |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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111 #if str( $library.aligned_file ) == "true": |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
|
112 #if $compressed == "GZ": |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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changeset
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113 --al-gz 'aligned_reads' |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
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114 #else if $compressed == "BZ2": |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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changeset
|
115 --al-bz2 'aligned_reads' |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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116 #else: |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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changeset
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117 --al 'aligned_reads' |
|
16
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
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diff
changeset
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118 #end if |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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119 #end if |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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diff
changeset
|
120 |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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121 #else: |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
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122 -1 '${read1}' |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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123 -2 '${read2}' |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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124 #if str( $library.unaligned_file ) == "true": |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
125 #if $compressed == "GZ": |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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diff
changeset
|
126 --un-conc-gz 'unaligned_reads' |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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127 #else if $compressed == "BZ2": |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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diff
changeset
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128 --un-conc-bz2 'unaligned_reads' |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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129 #else: |
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33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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changeset
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130 --un-conc 'unaligned_reads' |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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131 #end if |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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132 #end if |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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133 #if str( $library.aligned_file ) == "true": |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
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134 #if $compressed == "GZ": |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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diff
changeset
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135 --al-conc-gz 'aligned_reads' |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
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136 #else if $compressed == "BZ2": |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
137 --al-conc-bz2 'aligned_reads' |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
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138 #else: |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
139 --al-conc 'aligned_reads' |
| 0 | 140 #end if |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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141 #end if |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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142 #if str( $library.paired_options.paired_options_selector ) == "yes": |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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143 -I ${library.paired_options.I} |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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144 -X ${library.paired_options.X} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
|
145 ${library.paired_options.fr_rf_ff} |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
|
146 ${library.paired_options.no_mixed} |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
changeset
|
147 ${library.paired_options.no_discordant} |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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148 ${library.paired_options.dovetail} |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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diff
changeset
|
149 ${library.paired_options.no_contain} |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
|
150 ${library.paired_options.no_overlap} |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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151 #end if |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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diff
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|
152 #end if |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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diff
changeset
|
153 |
|
18
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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154 ## Read group information. |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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changeset
|
155 @define_read_group_helpers@ |
|
e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
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156 #if str( $library.type ) == "single": |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents:
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changeset
|
157 #set $rg_auto_name = $read_group_name_default($library.input_1) |
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e0ca9500999b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
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158 #else |
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159 #set $rg_auto_name = $read_group_name_default($library.input_1) |
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160 #end if |
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161 @set_use_rg_var@ |
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162 @set_read_group_vars@ |
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163 #if $use_rg |
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164 $format_read_group("", $rg_id, '"', arg='--rg-id ') |
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165 $format_read_group("SM:", $rg_sm, '"', arg='--rg ') |
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166 $format_read_group("PL:", $rg_pl, '"', arg='--rg ') |
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167 $format_read_group("LB:", $rg_lb, '"', arg='--rg ') |
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168 $format_read_group("CN:", $rg_cn, '"', arg='--rg ') |
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169 $format_read_group("DS:", $rg_ds, '"', arg='--rg ') |
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170 $format_read_group("DT:", $rg_dt, '"', arg='--rg ') |
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171 $format_read_group("FO:", $rg_fo, '"', arg='--rg ') |
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172 $format_read_group("KS:", $rg_ks, '"', arg='--rg ') |
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173 $format_read_group("PG:", $rg_pg, '"', arg='--rg ') |
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174 $format_read_group("PI:", $rg_pi, '"', arg='--rg ') |
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175 $format_read_group("PU:", $rg_pu, '"', arg='--rg ') |
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176 #end if |
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177 |
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178 ## Analysis type |
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179 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ): |
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180 $analysis_type.presets |
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181 #elif str( $analysis_type.analysis_type_selector ) == "full": |
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182 #if str( $analysis_type.input_options.input_options_selector ) == "yes": |
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183 --skip ${analysis_type.input_options.skip} |
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184 --qupto ${analysis_type.input_options.qupto} |
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185 --trim5 ${analysis_type.input_options.trim5} |
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186 --trim3 ${analysis_type.input_options.trim3} |
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187 ${analysis_type.input_options.qv_encoding} |
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188 ${analysis_type.input_options.solexa_quals} |
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189 ${analysis_type.input_options.int_quals} |
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190 #end if |
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191 |
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192 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes": |
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193 -N ${analysis_type.alignment_options.N} |
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194 -L ${analysis_type.alignment_options.L} |
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195 -i '${analysis_type.alignment_options.i}' |
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196 --n-ceil '${analysis_type.alignment_options.n_ceil}' |
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197 --dpad ${analysis_type.alignment_options.dpad} |
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198 --gbar ${analysis_type.alignment_options.gbar} |
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199 ${analysis_type.alignment_options.ignore_quals} |
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200 ${analysis_type.alignment_options.nofw} |
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201 ${analysis_type.alignment_options.norc} |
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202 ${analysis_type.alignment_options.no_1mm_upfront} |
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203 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end": |
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204 --end-to-end |
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205 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}' |
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206 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local": |
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207 --local |
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208 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}' |
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209 #end if |
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210 #end if |
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211 |
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212 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes": |
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213 #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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214 --ma ${analysis_type.scoring_options.ma} |
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215 #end if |
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216 --mp '${analysis_type.scoring_options.mp}' |
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217 --np ${analysis_type.scoring_options.np} |
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218 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend} |
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219 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend} |
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220 #end if |
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221 |
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222 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k": |
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223 -k ${analysis_type.reporting_options.k} |
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224 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a": |
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225 -a |
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226 #end if |
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227 |
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228 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": |
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229 -D ${analysis_type.effort_options.D} |
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230 -R ${analysis_type.effort_options.R} |
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231 #end if |
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232 #if str( $analysis_type.other_options.other_options_selector ) == "yes": |
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233 ${analysis_type.other_options.non_deterministic} |
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234 --seed ${analysis_type.other_options.seed} |
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235 #end if |
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236 |
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237 #elif str( $analysis_type.analysis_type_selector ) == "cline": |
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238 ${analysis_type.cline} |
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239 #end if |
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240 |
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241 #if str( $sam_options.sam_options_selector ) == "yes": |
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242 ${sam_options.no_unal} |
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243 ${sam_options.omit_sec_seq} |
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244 ${sam_options.sam_no_qname_trunc} |
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245 ${sam_options.xeq} |
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246 ${sam_options.soft_clipped_unmapped_tlen} |
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247 ${sam_options.reorder} |
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248 #end if |
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249 |
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250 ## mapping stats (i.e. stderr from bowtie2) |
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251 #if $save_mapping_stats |
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252 2> >(tee '$mapping_stats' >&2) |
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253 #end if |
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254 |
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255 ## output file |
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256 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''): |
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257 ## Convert SAM output to sorted BAM |
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258 ## using the two pipe stages has the following effect |
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259 ## - mapping and sorting run in parallel, during this time sort produces |
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260 ## presorted temporary files but does not produce output (hence |
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261 ## view does not run) |
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262 ## - once mapping is finished sort will start to merge the temporary |
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263 ## files (which should be fast also on a single thread) gives the |
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264 ## sorted output to view which only compresses the files (now |
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265 ## using full parallelism again) |
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266 | samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o '$output' |
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267 #else if $sam_options.reorder: |
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268 | samtools view --no-PG -b -o '$output' |
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269 #else: |
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270 > '$output' |
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271 #end if |
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272 ]]></command> |
| 0 | 273 <inputs> |
| 274 <!-- single/paired --> | |
| 275 <conditional name="library"> | |
| 2 | 276 <param name="type" type="select" label="Is this single or paired library"> |
| 0 | 277 <option value="single">Single-end</option> |
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278 <option value="paired_collection">Paired-end</option> |
| 0 | 279 </param> |
| 280 <when value="single"> | |
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281 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype "fastqsanger" or "fasta"" /> |
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282 <expand macro="align_unalign" /> |
| 0 | 283 </when> |
| 2 | 284 <when value="paired_collection"> |
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285 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" /> |
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286 <expand macro="align_unalign" /> |
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287 <expand macro="paired_end_options" /> |
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288 </when> |
| 0 | 289 </conditional> |
| 290 <!-- reference genome --> | |
| 291 <conditional name="reference_genome"> | |
| 2 | 292 <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"> |
| 293 <option value="indexed">Use a built-in genome index</option> | |
| 294 <option value="history">Use a genome from the history and build index</option> | |
| 0 | 295 </param> |
| 296 <when value="indexed"> | |
| 2 | 297 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
| 0 | 298 <options from_data_table="bowtie2_indexes"> |
| 299 <filter type="sort_by" column="2"/> | |
| 300 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 301 </options> | |
| 302 </param> | |
| 303 </when> | |
| 304 <when value="history"> | |
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305 <param name="own_file" type="data" format="fasta" label="Select reference genome" /> |
| 0 | 306 </when> |
| 307 </conditional> | |
| 2 | 308 <!-- read group settings --> |
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309 <expand macro="read_group_conditional" /> |
| 2 | 310 <conditional name="analysis_type"> |
| 311 <param name="analysis_type_selector" type="select" label="Select analysis mode"> | |
| 312 <option value="simple">1: Default setting only</option> | |
| 313 <option value="full">2: Full parameter list</option> | |
| 0 | 314 </param> |
| 2 | 315 <when value="simple"> |
| 316 <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."> | |
| 317 <option value="no_presets" selected="True">No, just use defaults</option> | |
| 318 <option value="--very-fast">Very fast end-to-end (--very-fast)</option> | |
| 319 <option value="--fast">Fast end-to-end (--fast)</option> | |
| 320 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option> | |
| 321 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option> | |
| 322 <option value="--very-fast-local">Very fast local (--very-fast-local)</option> | |
| 323 <option value="--fast-local">Fast local (--fast-local)</option> | |
| 324 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option> | |
| 325 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option> | |
| 0 | 326 </param> |
| 2 | 327 </when> |
| 328 <when value="full"> | |
| 329 <conditional name="input_options"> | |
| 330 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See "Input Options" section of Help below for information"> | |
| 331 <option value="yes">Yes</option> | |
| 332 <option value="no" selected="true">No</option> | |
| 333 </param> | |
| 334 <when value="yes"> | |
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335 <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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336 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/> |
| 2 | 337 <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"/> |
| 338 <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"/> | |
| 339 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details"> | |
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340 <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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341 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option> |
| 2 | 342 </param> |
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343 <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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344 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/> |
| 2 | 345 </when> |
| 346 <when value="no"> | |
| 347 <!-- do nothing --> | |
| 348 </when> | |
| 349 </conditional> | |
| 350 <conditional name="alignment_options"> | |
| 351 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See "Alignment Options" section of Help below for information"> | |
| 352 <option value="yes">Yes</option> | |
| 353 <option value="no" selected="true">No</option> | |
| 354 </param> | |
| 355 <when value="yes"> | |
| 356 <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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357 <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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358 <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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359 <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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360 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/> |
| 2 | 361 <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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362 <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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363 <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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364 <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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365 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/> |
| 2 | 366 <conditional name="align_mode"> |
| 367 <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"> | |
| 368 <option value="end-to-end" selected="True">End to End (--end-to-end)</option> | |
| 369 <option value="local">Local (--local)</option> | |
| 370 </param> | |
| 371 <when value="end-to-end"> | |
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372 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/> |
| 2 | 373 </when> |
| 374 <when value="local"> | |
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375 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/> |
| 2 | 376 </when> |
| 377 </conditional> | |
| 378 </when> | |
| 379 <when value="no"> | |
| 380 <!-- do nothing --> | |
| 381 </when> | |
| 382 </conditional> | |
| 383 <conditional name="scoring_options"> | |
| 384 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See "Scoring Options" section of Help below for information"> | |
| 385 <option value="yes">Yes</option> | |
| 386 <option value="no" selected="true">No</option> | |
| 387 </param> | |
| 388 <when value="yes"> | |
| 389 <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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390 <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/> |
| 2 | 391 <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"/> |
| 392 <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"/> | |
| 393 <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"/> | |
| 394 <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"/> | |
| 395 <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"/> | |
| 396 </when> | |
| 397 <when value="no"> | |
| 398 <!-- do nothing --> | |
| 399 </when> | |
| 400 </conditional> | |
| 401 <conditional name="reporting_options"> | |
| 402 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See "Reporting Options" section of Help below for information on -k and -a options"> | |
| 403 <option value="no" selected="true">No, do not set</option> | |
| 404 <option value="k">Set -k option and enter -k value</option> | |
| 405 <option value="a">Set -a option</option> | |
| 406 </param> | |
| 407 <when value="no"> | |
| 408 <!-- do nothing --> | |
| 409 </when> | |
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410 <when value="k"> |
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411 <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 | 412 </when> |
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413 <when value="a"> |
| 2 | 414 <!-- do nothing here; set -a flag on the command line--> |
| 415 </when> | |
| 416 </conditional> | |
| 417 <conditional name="effort_options"> | |
| 418 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See "Effort Options" section of Help below for information"> | |
| 419 <option value="yes">Yes</option> | |
| 420 <option value="no" selected="true">No</option> | |
| 421 </param> | |
| 422 <when value="yes"> | |
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423 <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 | 424 <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"/> |
| 425 </when> | |
| 426 <when value="no"> | |
| 427 <!-- do nothing --> | |
| 428 </when> | |
| 429 </conditional> | |
| 430 <conditional name="other_options"> | |
| 431 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See "Other Options" section of Help below for information"> | |
| 432 <option value="yes">Yes</option> | |
| 433 <option value="no" selected="true">No</option> | |
| 434 </param> | |
| 435 <when value="yes"> | |
| 436 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/> | |
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437 <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 | 438 </when> |
| 439 <when value="no"> | |
| 440 <!-- do nothing --> | |
| 441 </when> | |
| 442 </conditional> | |
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443 </when> |
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444 </conditional> |
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445 <conditional name="sam_options"> |
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446 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See "Output Options" section of Help below for information"> |
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447 <option value="yes">Yes</option> |
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448 <option value="no" selected="true">No</option> |
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449 </param> |
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450 <when value="yes"> |
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451 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/> |
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452 <param argument="--no-unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/> |
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453 <param argument="--omit-sec-seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/> |
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454 <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/> |
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455 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/> |
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456 <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/> |
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457 <param argument="--reorder" type="boolean" truevalue="--reorder" falsevalue="" |
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458 label="Reorder output to reflect order of the input file" |
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459 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 | 460 </when> |
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461 <when value="no"/> |
| 0 | 462 </conditional> |
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463 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" /> |
| 0 | 464 </inputs> |
| 465 <!-- define outputs --> | |
| 466 <outputs> | |
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467 <data name="output_unaligned_reads" format_source="library|input_1" from_work_dir="unaligned_reads" label="${tool.name} on ${on_string}: unaligned reads" > |
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468 <filter>library['type'] == 'single' and library['unaligned_file'] is True</filter> |
| 0 | 469 <actions> |
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470 <expand macro="dbKeyActions" /> |
| 0 | 471 </actions> |
| 472 </data> | |
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473 <collection name="output_unaligned_read_pairs" type="paired" label="${tool.name} on ${on_string}: unaligned read pairs"> |
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474 <filter>library['type'] != 'single' and library['unaligned_file'] is True</filter> |
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475 <data name="forward" from_work_dir="unaligned_reads.1" format_source="library|input_1['forward']"> |
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476 <actions> |
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477 <expand macro="dbKeyActions" /> |
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478 </actions> |
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479 </data> |
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480 <data name="reverse" from_work_dir="unaligned_reads.2" format_source="library|input_1['reverse']"> |
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481 <actions> |
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482 <expand macro="dbKeyActions" /> |
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483 </actions> |
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484 </data> |
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485 </collection> |
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486 |
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487 <data name="output_aligned_reads" format_source="library|input_1" from_work_dir="aligned_reads" label="${tool.name} on ${on_string}: aligned reads" > |
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488 <filter>library['type'] == 'single' and library['aligned_file'] is True</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
489 <actions> |
|
23
5e52e98ff239
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents:
22
diff
changeset
|
490 <expand macro="dbKeyActions" /> |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
491 </actions> |
|
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents:
10
diff
changeset
|
492 </data> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
493 <collection name="output_aligned_read_pairs" type="paired" label="${tool.name} on ${on_string}: aligned read pairs"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
494 <filter>library['type'] != 'single' and library['aligned_file'] is True</filter> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
495 <data name="forward" from_work_dir="aligned_reads.1" format_source="library|input_1['forward']"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
496 <actions> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
497 <expand macro="dbKeyActions" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
498 </actions> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
499 </data> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
500 <data name="reverse" from_work_dir="aligned_reads.2" format_source="library|input_1['forward']"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
501 <actions> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
502 <expand macro="dbKeyActions" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
503 </actions> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
504 </data> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
505 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
506 |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
507 <data name="output" format="bam" label="${tool.name} on ${on_string}: alignments"> |
|
22
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
508 <change_format> |
|
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
509 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" /> |
|
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
510 <when input="sam_options.sam_opt" value="true" format="sam" /> |
|
22
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
511 </change_format> |
| 0 | 512 <actions> |
| 513 <conditional name="reference_genome.source"> | |
| 514 <when value="indexed"> | |
| 515 <action type="metadata" name="dbkey"> | |
| 516 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> | |
| 517 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | |
| 518 <filter type="param_value" ref="reference_genome.index" column="0"/> | |
| 519 </option> | |
| 520 </action> | |
| 521 </when> | |
| 522 <when value="history"> | |
| 523 <action type="metadata" name="dbkey"> | |
| 524 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> | |
| 525 </action> | |
| 526 </when> | |
| 527 </conditional> | |
|
23
5e52e98ff239
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents:
22
diff
changeset
|
528 <expand macro="dbKeyActions" /> |
| 0 | 529 </actions> |
| 530 </data> | |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
531 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats"> |
|
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
532 <filter>save_mapping_stats is True</filter> |
|
23
5e52e98ff239
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents:
22
diff
changeset
|
533 <actions> |
|
5e52e98ff239
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents:
22
diff
changeset
|
534 <expand macro="dbKeyActions" /> |
|
5e52e98ff239
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7
iuc
parents:
22
diff
changeset
|
535 </actions> |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
536 </data> |
| 0 | 537 </outputs> |
| 538 <tests> | |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
539 <!-- test on single-end datasets --> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
540 <test expect_num_outputs="2"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
541 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
542 <param name="type" value="single"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
543 <param name="unaligned_file" value="true"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
544 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
545 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
546 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
547 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
548 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
549 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
550 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
551 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
552 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
553 <output name="output_unaligned_reads" ftype="fastqsanger"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
554 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
555 <has_n_lines n="312"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
556 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
557 </output> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
558 <output name="output" file="bowtie2-single.bam" ftype="bam" lines_diff="4" sort="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
559 <metadata name="sort_order" value="coordinate"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
560 </output> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
561 </test> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
562 <!-- test on paired-end datasets --> |
|
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
563 <test expect_num_outputs="1"> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
564 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
565 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
566 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
567 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
568 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
569 <param name="unaligned_file" value="false"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
570 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
571 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
572 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
573 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
574 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
575 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
576 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
577 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
578 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
579 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
580 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
581 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
582 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
583 </conditional> |
|
31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
584 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
585 <metadata name="sort_order" value="coordinate"/> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
586 </output> |
| 0 | 587 </test> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
588 <!-- test on paired-end datasets + unaligned output --> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
589 <test expect_num_outputs="4"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
590 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
591 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
592 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
593 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
594 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
595 <param name="unaligned_file" value="true"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
596 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
597 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
598 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
599 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
600 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
601 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
602 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
603 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
604 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
605 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
606 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
607 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
608 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
609 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
610 <output_collection name="output_unaligned_read_pairs" type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
611 <element name="forward" ftype="fastqsanger"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
612 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
613 <has_n_lines n="388"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
614 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
615 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
616 <element name="reverse" ftype="fastqsanger"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
617 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
618 <has_n_lines n="388"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
619 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
620 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
621 </output_collection> |
|
31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
622 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
623 <metadata name="sort_order" value="coordinate"/> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
624 </output> |
|
17
69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents:
16
diff
changeset
|
625 </test> |
|
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
626 <test expect_num_outputs="1"> |
|
17
69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents:
16
diff
changeset
|
627 <!-- test on paired-end datasets with read group info --> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
628 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
629 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
630 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
631 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
632 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
633 <param name="unaligned_file" value="false"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
634 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
635 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
636 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
637 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
638 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
639 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
640 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
641 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
642 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
643 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
644 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
645 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
646 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
647 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
648 <conditional name="sam_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
649 <param name="sam_options_selector" value="yes" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
650 <param name="sam_opt" value="true" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
651 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
652 <conditional name="rg"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
653 <param name="rg_selector" value="set"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
654 <conditional name="read_group_id_conditional"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
655 <param name="do_auto_name" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
656 <param name="ID" value="rg1"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
657 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
658 <param name="PL" value="CAPILLARY"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
659 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
660 <output name="output" ftype="sam" lines_diff="4" sort="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
661 <metadata name="sort_order" value="unsorted"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
662 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
663 <has_line line="@RG	ID:rg1	PL:CAPILLARY"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
664 <has_text text="RG:Z:rg1" n="200"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
665 </assert_contents> |
|
31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
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diff
changeset
|
666 </output> |
|
5
5cfa4b6db588
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
667 </test> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
668 <!-- test on paired-end datasets with stats output --> |
|
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
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diff
changeset
|
669 <test expect_num_outputs="2"> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
670 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
671 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
672 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
673 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
674 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
675 <param name="unaligned_file" value="false"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
676 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
677 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
678 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
679 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
680 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
681 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
682 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
683 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
684 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
685 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
686 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
687 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
688 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
689 </conditional> |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
690 <param name="save_mapping_stats" value="true" /> |
|
31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
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diff
changeset
|
691 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
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diff
changeset
|
692 <metadata name="sort_order" value="coordinate"/> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
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diff
changeset
|
693 </output> |
|
15
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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diff
changeset
|
694 <output name="mapping_stats"> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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diff
changeset
|
695 <assert_contents> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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diff
changeset
|
696 <has_text text="of these" /> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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diff
changeset
|
697 </assert_contents> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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diff
changeset
|
698 </output> |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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diff
changeset
|
699 </test> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
700 <!-- test on fastqsanger.gz paired-end datasets plus reference from data table --> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
701 <test expect_num_outputs="4"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
702 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
703 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
704 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
705 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
706 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
707 <param name="unaligned_file" value="true"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
708 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
709 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
710 <element name="forward" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
711 <element name="reverse" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
712 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
713 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
714 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
715 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
716 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
717 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
718 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
719 <param name="source" value="indexed" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
720 <param name="index" value="test_value" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
721 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
722 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> |
|
31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
723 <metadata name="sort_order" value="coordinate"/> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
724 </output> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
725 <output_collection name="output_unaligned_read_pairs" type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
726 <element name="forward" ftype="fastqsanger.gz" decompress="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
727 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
728 <has_n_lines n="388"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
729 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
730 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
731 <element name="reverse" ftype="fastqsanger.gz" decompress="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
732 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
733 <has_n_lines n="388"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
734 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
735 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
736 </output_collection> |
|
10
fed480fea9f0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
8
diff
changeset
|
737 </test> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
738 <!-- test on fastqsanger.bz2 paired-end datasets --> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
739 <test expect_num_outputs="4"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
740 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
741 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
742 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
743 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
744 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
745 <param name="aligned_file" value="true"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
746 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
747 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
748 <element name="forward" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
749 <element name="reverse" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
750 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
751 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
752 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
753 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
754 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
755 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
756 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
757 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
758 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
759 </conditional> |
|
31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
760 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
761 <metadata name="sort_order" value="coordinate"/> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
762 </output> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
763 <output_collection name="output_aligned_read_pairs" type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
764 <element name="forward" ftype="fastqsanger.bz2" decompress="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
765 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
766 <has_n_lines n="12"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
767 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
768 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
769 <element name="reverse" ftype="fastqsanger.bz2" decompress="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
770 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
771 <has_n_lines n="12"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
772 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
773 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
774 </output_collection> |
|
14
85f0e9edb32d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents:
13
diff
changeset
|
775 </test> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
776 <!-- test on fasta paired-end datasets + aligned + unaligned --> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
777 <test expect_num_outputs="7"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
778 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
779 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
780 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
781 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
782 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
783 <param name="unaligned_file" value="true"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
784 <param name="aligned_file" value="true"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
785 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
786 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
787 <element name="forward" value="bowtie2-fq1.fa" ftype="fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
788 <element name="reverse" value="bowtie2-fq2.fa" ftype="fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
789 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
790 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
791 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
792 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
793 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
794 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
795 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
796 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
797 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
798 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
799 |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
800 <output_collection name="output_unaligned_read_pairs" type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
801 <element name="forward" ftype="fasta" decompress="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
802 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
803 <has_n_lines n="194"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
804 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
805 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
806 <element name="reverse" ftype="fasta" decompress="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
807 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
808 <has_n_lines n="194"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
809 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
810 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
811 </output_collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
812 <output_collection name="output_aligned_read_pairs" type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
813 <element name="forward" ftype="fasta" decompress="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
814 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
815 <has_n_lines n="6"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
816 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
817 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
818 <element name="reverse" ftype="fasta" decompress="true"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
819 <assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
820 <has_n_lines n="6"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
821 </assert_contents> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
822 </element> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
823 </output_collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
824 |
|
31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
825 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4" sort="true"> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
826 <metadata name="sort_order" value="coordinate"/> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
827 </output> |
|
16
def46fdb3909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents:
15
diff
changeset
|
828 </test> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
829 <!-- test on fasta paired-end datasets with bam_native as output --> |
|
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
830 <test expect_num_outputs="1"> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
831 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
832 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
833 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
834 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
835 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
836 <param name="unaligned_file" value="false"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
837 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
838 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
839 <element name="forward" value="bowtie2-fq1.fa" ftype="fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
840 <element name="reverse" value="bowtie2-fq2.fa" ftype="fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
841 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
842 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
843 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
844 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
845 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
846 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
847 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
848 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
849 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
850 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
851 <conditional name="sam_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
852 <param name="sam_options_selector" value="yes" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
853 <param name="reorder" value="true" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
854 </conditional> |
|
31
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
855 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" lines_diff="4"> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
856 <metadata name="sort_order" value="unsorted"/> |
|
f66e4858ca26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
30
diff
changeset
|
857 </output> |
|
22
b2f8e8b8b9a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents:
21
diff
changeset
|
858 </test> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
859 <!-- test on fasta paired-end datasets with sam as output --> |
|
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
23
diff
changeset
|
860 <test expect_num_outputs="1"> |
|
33
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
861 <conditional name="library"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
32
diff
changeset
|
862 <param name="type" value="paired_collection"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
863 <conditional name="paired_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
864 <param name="paired_options_selector" value="no"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
865 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
866 <param name="unaligned_file" value="false"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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changeset
|
867 <param name="input_1"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
868 <collection type="paired"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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diff
changeset
|
869 <element name="forward" value="bowtie2-fq1.fa" ftype="fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
870 <element name="reverse" value="bowtie2-fq2.fa" ftype="fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
871 </collection> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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changeset
|
872 </param> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
873 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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changeset
|
874 <conditional name="analysis_type"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
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|
875 <param name="analysis_type_selector" value="simple"/> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
876 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
877 <conditional name="reference_genome"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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diff
changeset
|
878 <param name="source" value="history" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
879 <param name="own_file" value="bowtie2-ref.fasta" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
changeset
|
880 </conditional> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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diff
changeset
|
881 <conditional name="sam_options"> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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|
882 <param name="sam_options_selector" value="yes" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
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|
883 <param name="sam_opt" value="true" /> |
|
c3d19e7ee879
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
iuc
parents:
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diff
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|
884 </conditional> |
|
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
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diff
changeset
|
885 <output name="output" ftype="sam"> |
|
31
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
iuc
parents:
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changeset
|
886 <metadata name="sort_order" value="unsorted"/> |
|
24
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
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|
887 <assert_contents> |
|
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
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|
888 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" /> |
|
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
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|
889 </assert_contents> |
|
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
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|
890 </output> |
|
cd8b7d755af8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
iuc
parents:
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|
891 </test> |
| 0 | 892 </tests> |
|
11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff
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|
893 <help><![CDATA[ |
| 0 | 894 **Bowtie2 Overview** |
|
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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parents:
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|
895 |
| 2 | 896 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. |
| 897 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead. | |
| 898 | |
| 899 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/ | |
| 900 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml | |
| 901 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf | |
| 902 | |
| 903 ----- | |
| 0 | 904 |
| 2 | 905 **Selecting reference genomes for Bowtie2** |
| 906 | |
| 907 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 | 908 |
|
11
fa69d5a7b8c8
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changeset
|
909 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 | 910 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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911 |
| 2 | 912 If your genome of interest is not listed here you have two choices: |
| 913 | |
| 914 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 | |
| 915 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 | 916 |
| 917 ------ | |
| 918 | |
| 2 | 919 .. class:: infomark |
| 920 | |
| 921 **Bowtie2 options** | |
| 922 | |
| 923 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below. | |
| 924 | |
| 925 ----- | |
| 926 | |
| 0 | 927 **Inputs** |
| 928 | |
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929 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section). |
| 0 | 930 |
| 931 ------ | |
| 932 | |
| 2 | 933 **Input options**:: |
| 934 | |
|
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935 --interleaved |
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936 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair. |
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937 |
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938 -s/--skip <int> |
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939 Skip (i.e. do not align) the first `<int>` reads or pairs in the input. |
| 2 | 940 |
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941 -u/--qupto <int> |
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942 Align the first `<int>` reads or read pairs from the input (after the |
| 2 | 943 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit. |
| 944 | |
|
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945 -5/--trim5 <int> |
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946 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0). |
| 0 | 947 |
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948 -3/--trim3 <int> |
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949 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0). |
| 2 | 950 |
| 951 --phred33 | |
| 952 Input qualities are ASCII chars equal to the Phred quality plus 33. This is | |
| 953 also called the "Phred+33" encoding, which is used by the very latest Illumina | |
| 954 pipelines. | |
| 955 | |
| 956 --phred64 | |
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957 Input qualities are ASCII chars equal to the Phred quality plus 64. This is |
| 2 | 958 also called the "Phred+64" encoding. |
| 0 | 959 |
| 2 | 960 --solexa-quals |
| 961 Convert input qualities from Solexa Phred quality (which can be negative) to | |
| 962 Phred Phred quality (which can't). This scheme was used in older Illumina GA | |
| 963 Pipeline versions (prior to 1.3). Default: off. | |
| 964 | |
| 965 --int-quals | |
| 966 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`.... | |
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967 Integers are treated as being on the Phred quality scale unless |
| 2 | 968 `--solexa-quals` is also specified. Default: off. |
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969 |
| 2 | 970 ------ |
| 971 | |
| 972 **Presets in `--end-to-end` mode**:: | |
| 973 | |
| 974 --very-fast | |
| 975 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50` | |
| 976 | |
| 977 --fast | |
| 978 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50` | |
|
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979 |
| 2 | 980 --sensitive |
| 981 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode) | |
| 982 | |
| 983 --very-sensitive | |
| 984 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
| 0 | 985 |
| 986 ------ | |
| 987 | |
| 2 | 988 **Presets options in `--local` mode**:: |
| 0 | 989 |
| 2 | 990 --very-fast-local |
| 991 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00` | |
| 0 | 992 |
| 2 | 993 --fast-local |
| 994 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75` | |
| 0 | 995 |
| 2 | 996 --sensitive-local |
| 997 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode) | |
| 0 | 998 |
| 2 | 999 --very-sensitive-local |
| 1000 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
|
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1001 |
| 0 | 1002 ------ |
| 1003 | |
| 2 | 1004 **Alignment options**:: |
| 1005 | |
|
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1006 -N <int> |
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1007 Sets the number of mismatches to allowed in a seed alignment during multiseed |
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1008 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower |
| 2 | 1009 (often much slower) but increases sensitivity. Default: 0. |
| 1010 | |
|
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1011 -L <int> |
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1012 Sets the length of the seed substrings to align during multiseed alignment. |
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1013 Smaller values make alignment slower but more sensitive. Default: the |
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1014 `--sensitive` preset is used by default, which sets `-L` to 22 in |
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1015 `--end-to-end` mode and to 20 in `--local` mode. |
| 2 | 1016 |
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1017 -i <func> |
| 2 | 1018 Sets a function governing the interval between seed substrings to use during |
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1019 multiseed alignment. For instance, if the read has 30 characers, and seed |
| 2 | 1020 length is 10, and the seed interval is 6, the seeds extracted will be: |
| 1021 | |
| 1022 Read: TAGCTACGCTCTACGCTATCATGCATAAAC | |
| 1023 Seed 1 fw: TAGCTACGCT | |
| 1024 Seed 1 rc: AGCGTAGCTA | |
| 1025 Seed 2 fw: CGCTCTACGC | |
| 1026 Seed 2 rc: GCGTAGAGCG | |
| 1027 Seed 3 fw: ACGCTATCAT | |
| 1028 Seed 3 rc: ATGATAGCGT | |
| 1029 Seed 4 fw: TCATGCATAA | |
| 1030 Seed 4 rc: TTATGCATGA | |
| 1031 | |
| 1032 Since it's best to use longer intervals for longer reads, this parameter sets | |
| 1033 the interval as a function of the read length, rather than a single | |
| 1034 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the | |
| 1035 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. | |
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1036 If the function returns a result less than |
| 2 | 1037 1, it is rounded up to 1. Default: the `--sensitive` preset is used by |
| 1038 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75` | |
| 1039 in `--local` mode. | |
| 1040 | |
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1041 --n-ceil <func> |
| 2 | 1042 Sets a function governing the maximum number of ambiguous characters (usually |
| 1043 `N`s and/or `.`s) allowed in a read as a function of read length. For instance, | |
| 1044 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, | |
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1045 where x is the read length. Reads exceeding this ceiling are filtered out. |
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1046 Default: `L,0,0.15`. |
| 2 | 1047 |
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1048 --dpad <int> |
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1049 "Pads" dynamic programming problems by `<int>` columns on either side to allow |
| 2 | 1050 gaps. Default: 15. |
| 1051 | |
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1052 --gbar <int> |
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1053 Disallow gaps within `<int>` positions of the beginning or end of the read. |
| 2 | 1054 Default: 4. |
| 1055 | |
| 1056 --ignore-quals | |
| 1057 When calculating a mismatch penalty, always consider the quality value at the | |
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1058 mismatched position to be the highest possible, regardless of the actual value. |
| 2 | 1059 I.e. input is treated as though all quality values are high. This is also the |
| 1060 default behavior when the input doesn't specify quality values (e.g. in `-f`, | |
| 1061 `-r`, or `-c` modes). | |
| 0 | 1062 |
| 2 | 1063 --nofw/--norc |
| 1064 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to | |
| 1065 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will | |
| 1066 not attempt to align unpaired reads against the reverse-complement (Crick) | |
| 1067 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the | |
| 1068 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those | |
| 1069 paired-end configurations corresponding to fragments from the reverse-complement | |
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1070 (Crick) strand. Default: both strands enabled. |
| 2 | 1071 |
| 1072 --no-1mm-upfront | |
| 1073 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch | |
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1074 end-to-end alignment for the read *before* trying the multiseed heuristic. Such |
| 2 | 1075 alignments can be found very quickly, and many short read alignments have exact or |
| 1076 near-exact end-to-end alignments. However, this can lead to unexpected | |
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1077 alignments when the user also sets options governing the multiseed heuristic, |
| 2 | 1078 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal |
| 1079 to the length of the read, the user will be surprised to find 1-mismatch alignments | |
| 1080 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end | |
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1081 alignments before using the multiseed heuristic, which leads to the expected |
| 2 | 1082 behavior when combined with options such as `-L` and `-N`. This comes at the |
| 1083 expense of speed. | |
| 1084 | |
| 1085 --end-to-end | |
| 1086 In this mode, Bowtie 2 requires that the entire read align from one end to the | |
| 1087 other, without any trimming (or "soft clipping") of characters from either end. | |
| 1088 The match bonus `--ma` always equals 0 in this mode, so all alignment scores | |
| 1089 are less than or equal to 0, and the greatest possible alignment score is 0. | |
| 1090 This is mutually exclusive with `--local`. `--end-to-end` is the default mode. | |
| 0 | 1091 |
| 2 | 1092 --local |
| 1093 In this mode, Bowtie 2 does not require that the entire read align from one end | |
| 1094 to the other. Rather, some characters may be omitted ("soft clipped") from the | |
| 1095 ends in order to achieve the greatest possible alignment score. The match bonus | |
| 1096 `--ma` is used in this mode, and the best possible alignment score is equal to | |
| 1097 the match bonus (`--ma`) times the length of the read. Specifying `--local` | |
| 1098 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying | |
| 1099 the local version of the preset (`--very-fast-local`). This is mutually | |
| 1100 exclusive with `--end-to-end`. `--end-to-end` is the default mode. | |
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1101 |
| 2 | 1102 ----- |
| 1103 | |
| 1104 **Scoring options**:: | |
| 1105 | |
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1106 --ma <int> |
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1107 Sets the match bonus. In `--local` mode `<int>` is added to the alignment |
| 2 | 1108 score for each position where a read character aligns to a reference character |
| 1109 and the characters match. Not used in `--end-to-end` mode. Default: 2. | |
| 1110 | |
| 1111 --mp MX,MN | |
| 1112 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A | |
| 1113 number less than or equal to `MX` and greater than or equal to `MN` is | |
| 1114 subtracted from the alignment score for each position where a read character | |
| 1115 aligns to a reference character, the characters do not match, and neither is an | |
| 1116 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. | |
| 1117 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` | |
| 1118 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2. | |
| 1119 | |
|
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1120 --np <int> |
| 2 | 1121 Sets penalty for positions where the read, reference, or both, contain an |
| 1122 ambiguous character such as `N`. Default: 1. | |
| 1123 | |
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1124 --rdg <int1>,<int2> |
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1125 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of |
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1126 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3. |
| 2 | 1127 |
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1128 --rfg <int1>,<int2> |
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1129 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A |
|
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1130 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default: |
| 2 | 1131 5, 3. |
| 0 | 1132 |
|
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1133 --score-min <func> |
| 2 | 1134 Sets a function governing the minimum alignment score needed for an alignment to |
| 1135 be considered "valid" (i.e. good enough to report). This is a function of read | |
| 1136 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` | |
|
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1137 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 | 1138 the default in `--local` mode is `G,20,8`. |
|
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1139 |
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1140 ----- |
| 2 | 1141 |
| 1142 **Reporting options**:: | |
| 1143 | |
|
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1144 -k <int> |
| 2 | 1145 By default, `bowtie2` searches for distinct, valid alignments for each read. |
| 1146 When it finds a valid alignment, it continues looking for alignments that are | |
| 1147 nearly as good or better. The best alignment found is reported (randomly | |
| 1148 selected from among best if tied). Information about the best alignments is | |
| 1149 used to estimate mapping quality and to set SAM optional fields, such as | |
| 1150 `AS:i` and `XS:i`. | |
| 1151 | |
| 1152 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it | |
|
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1153 searches for at most `<int>` distinct, valid alignments for each read. The |
| 2 | 1154 search terminates when it can't find more distinct valid alignments, or when it |
|
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1155 finds `<int>`, whichever happens first. All alignments found are reported in |
| 2 | 1156 descending order by alignment score. The alignment score for a paired-end |
| 1157 alignment equals the sum of the alignment scores of the individual mates. Each | |
| 1158 reported read or pair alignment beyond the first has the SAM 'secondary' bit | |
| 1159 (which equals 256) set in its FLAGS field. For reads that have more than | |
|
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1160 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the |
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1161 `<int>` alignments reported are the best possible in terms of alignment score. |
| 2 | 1162 `-k` is mutually exclusive with `-a`. |
| 0 | 1163 |
| 2 | 1164 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when |
| 1165 aligning reads to long, repetitive genomes large `-k` can be very, very slow. | |
| 1166 | |
| 1167 -a | |
| 1168 Like `-k` but with no upper limit on number of alignments to search for. `-a` | |
| 1169 is mutually exclusive with `-k`. | |
| 1170 | |
| 1171 Note: Bowtie 2 is not designed with `-a` mode in mind, and when | |
| 1172 aligning reads to long, repetitive genomes this mode can be very, very slow. | |
|
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1173 |
| 2 | 1174 ----- |
| 1175 | |
| 1176 **Effort options**:: | |
| 1177 | |
|
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1178 -D <int> |
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1179 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2 |
| 2 | 1180 moves on, using the alignments found so far. A seed extension "fails" if it |
| 1181 does not yield a new best or a new second-best alignment. This limit is | |
| 1182 automatically adjusted up when -k or -a are specified. Default: 15. | |
| 1183 | |
|
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1184 -R <int> |
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1185 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with |
| 2 | 1186 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads |
| 1187 (same length, same number of mismatches allowed) at different offsets and | |
| 1188 searches for more alignments. A read is considered to have repetitive seeds if | |
| 1189 the total number of seed hits divided by the number of seeds that aligned at | |
| 1190 least once is greater than 300. Default: 2. | |
|
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1191 |
| 2 | 1192 ----- |
| 1193 | |
| 1194 **Paired-end options**:: | |
| 0 | 1195 |
|
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1196 -I/--minins <int> |
| 2 | 1197 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is |
| 1198 specified and a paired-end alignment consists of two 20-bp alignments in the | |
| 1199 appropriate orientation with a 20-bp gap between them, that alignment is | |
| 1200 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not | |
| 1201 be valid in that case. If trimming options `-3` or `-5` are also used, the | |
| 1202 `-I` constraint is applied with respect to the untrimmed mates. | |
| 1203 | |
| 1204 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
| 1205 run. This is because larger differences bewteen `-I` and `-X` require that | |
| 1206 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
| 1207 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
| 1208 efficient. | |
| 1209 | |
|
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1210 Default: 0 (essentially imposing no minimum) |
| 2 | 1211 |
|
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1212 -X/--maxins <int> |
| 2 | 1213 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100` |
| 1214 is specified and a paired-end alignment consists of two 20-bp alignments in the | |
| 1215 proper orientation with a 60-bp gap between them, that alignment is considered | |
| 1216 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in | |
| 1217 that case. If trimming options `-3` or `-5` are also used, the `-X` | |
| 1218 constraint is applied with respect to the untrimmed mates, not the trimmed | |
| 1219 mates. | |
| 1220 | |
| 1221 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
| 1222 run. This is because larger differences bewteen `-I` and `-X` require that | |
| 1223 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
| 1224 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
| 1225 efficient. | |
| 1226 | |
| 1227 Default: 500. | |
| 0 | 1228 |
| 2 | 1229 --fr/--rf/--ff |
| 1230 The upstream/downstream mate orientations for a valid paired-end alignment | |
| 1231 against the forward reference strand. E.g., if `--fr` is specified and there is | |
| 1232 a candidate paired-end alignment where mate 1 appears upstream of the reverse | |
| 1233 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are | |
| 1234 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse | |
| 1235 complement of mate 1 and all other constraints are met, that too is valid. | |
| 1236 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a | |
| 1237 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1 | |
| 1238 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate | |
| 1239 for Illumina's Paired-end Sequencing Assay). | |
| 1240 | |
| 1241 --no-mixed | |
| 1242 By default, when `bowtie2` cannot find a concordant or discordant alignment for | |
| 1243 a pair, it then tries to find alignments for the individual mates. This option | |
| 1244 disables that behavior. | |
| 0 | 1245 |
| 2 | 1246 --no-discordant |
| 1247 By default, `bowtie2` looks for discordant alignments if it cannot find any | |
| 1248 concordant alignments. A discordant alignment is an alignment where both mates | |
| 1249 align uniquely, but that does not satisfy the paired-end constraints | |
| 1250 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior. | |
| 1251 | |
| 1252 --dovetail | |
| 1253 If the mates "dovetail", that is if one mate alignment extends past the | |
| 1254 beginning of the other such that the wrong mate begins upstream, consider that | |
|
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1255 to be concordant. Default: mates cannot dovetail in a concordant alignment. |
| 2 | 1256 |
| 1257 --no-contain | |
| 1258 If one mate alignment contains the other, consider that to be non-concordant. | |
|
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1259 Default: a mate can contain the other in a concordant alignment. |
| 2 | 1260 |
| 1261 --no-overlap | |
| 1262 If one mate alignment overlaps the other at all, consider that to be | |
|
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1263 non-concordant. Default: mates can overlap in a concordant alignment. |
|
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1264 |
| 0 | 1265 ------ |
| 1266 | |
| 2 | 1267 **SAM options**:: |
| 0 | 1268 |
|
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1269 --rg-id <text> |
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1270 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be |
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1271 printed, with `<text>` as the value associated with the `ID:` tag. It also |
| 2 | 1272 causes the `RG:Z:` extra field to be attached to each SAM output record, with |
|
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1273 value set to `<text>`. |
| 0 | 1274 |
|
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1275 --rg <text> |
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1276 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the |
| 2 | 1277 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id` |
|
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1278 must also be specified. This is because the `ID` tag is required by the SAM |
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1279 Specification. Specify `--rg` multiple times to set multiple fields. See the |
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1280 SAM Specification for details about what fields are legal. |
| 0 | 1281 |
| 2 | 1282 --omit-sec-seq |
| 1283 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ` | |
| 1284 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix | |
| 1285 in those fields instead. | |
|
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1286 |
| 2 | 1287 ----- |
| 0 | 1288 |
| 2 | 1289 **Other options**:: |
| 0 | 1290 |
| 2 | 1291 --reorder |
| 1292 Guarantees that output SAM records are printed in an order corresponding to the | |
| 1293 order of the reads in the original input file, even when `-p` is set greater | |
| 1294 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie | |
| 1295 2 to run somewhat slower and use somewhat more memory then if `--reorder` were | |
| 1296 not specified. Has no effect if `-p` is set to 1, since output order will | |
| 1297 naturally correspond to input order in that case. | |
| 0 | 1298 |
|
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1299 --seed <int> |
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1300 Use `<int>` as the seed for pseudo-random number generator. Default: 0. |
| 0 | 1301 |
| 2 | 1302 --non-deterministic |
| 1303 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It | |
| 1304 seeds the generator with a number derived from (a) the read name, (b) the | |
| 1305 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed` | |
| 1306 option. This means that if two reads are identical (same name, same | |
| 1307 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s) | |
| 1308 for both, even if there was ambiguity. When `--non-deterministic` is specified, | |
| 1309 Bowtie 2 re-initializes its pseudo-random generator for each read using the | |
| 1310 current time. This means that Bowtie 2 will not necessarily report the same | |
| 1311 alignment for two identical reads. This is counter-intuitive for some users, | |
| 1312 but might be more appropriate in situations where the input consists of many | |
| 1313 identical reads. | |
| 0 | 1314 |
|
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1315 ----- |
|
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1316 |
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1317 |
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1318 **Paired-end (and mate-pair) data in fastq format** |
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1319 |
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1320 Paired end datasets can be represented as two individual datasets: |
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1321 |
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1322 First dataset:: |
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1323 |
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1324 @1/1 |
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1325 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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1326 + |
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1327 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED |
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1328 @2/1 |
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1329 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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1330 + |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff
changeset
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1331 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1332 |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1333 Second dataset:: |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1334 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1335 @1/2 |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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1336 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff
changeset
|
1337 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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1338 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1339 @2/2 |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1340 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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diff
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1341 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1342 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1343 |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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|
1344 Or a single *interleaved* dataset:: |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1345 |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1346 @1/1 |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1347 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1348 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1349 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1350 @1/2 |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1351 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1352 + |
|
7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1353 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1354 @2/1 |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1355 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1356 + |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1357 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1358 @2/2 |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1359 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1360 + |
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7e0b333f39e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1361 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH |
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11
fa69d5a7b8c8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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1362 ]]></help> |
| 2 | 1363 <citations> |
|
17
69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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1364 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> |
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69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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1365 <citation type="doi">10.1038/nmeth.1923</citation> |
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69f044db2445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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1366 </citations> |
| 0 | 1367 </tool> |