Mercurial > repos > iuc > bwameth
annotate bwameth.xml @ 10:cf1322aeb137 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 16f1bd9f85b90ad12dbb43bc00ebe469620cfd04
author | iuc |
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date | Sun, 02 Jun 2024 16:38:23 +0000 |
parents | d82648ad25a3 |
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rev | line source |
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8
62f5fab76dfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 2e16403caf8e83f7eb87a1c2155f20ae38b6d579"
iuc
parents:
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1 <tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy0" profile="20.05"> |
0
f7094efef903
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
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2 <description>Fast and accurate aligner of BS-Seq reads.</description> |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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3 <macros> |
10
cf1322aeb137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 16f1bd9f85b90ad12dbb43bc00ebe469620cfd04
iuc
parents:
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4 <token name="@TOOL_VERSION@">0.2.7</token> |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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5 </macros> |
0
f7094efef903
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
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6 <requirements> |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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7 <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement> |
0
f7094efef903
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff
changeset
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8 </requirements> |
f7094efef903
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff
changeset
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9 <version_command>bwameth.py --version</version_command> |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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10 <command detect_errors="aggressive"><![CDATA[ |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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11 #if $referenceSource.source != "indexed": |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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12 mkdir index_dir && |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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13 ln -s '$referenceSource.reference' index_dir/genome.fa && |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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14 bwameth.py index index_dir/genome.fa && |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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15 #set index="index_dir/genome.fa" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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16 #else |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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17 #set index=$referenceSource.index.fields.path |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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18 #end if |
0
f7094efef903
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
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19 |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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20 ## Link in the files with a name that's appropriate |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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21 #if str($single_or_paired.single_or_paired_opts) == 'paired': |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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22 #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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23 #set read1 = "input_f.fastq.gz" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
diff
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24 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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25 #set read1 = "input_f.fastq.bz2" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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26 #else: |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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27 #set read1 = "input_f.fastq" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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28 #end if |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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29 ln -f -s '${single_or_paired.input_mate1}' ${read1} && |
3
a6ea26c1f225
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
iuc
parents:
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30 |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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31 #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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32 #set read2 = "input_r.fastq.gz" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
diff
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33 #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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34 #set read2 = "input_r.fastq.bz2" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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35 #else: |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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36 #set read2 = "input_r.fastq" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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37 #end if |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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38 ln -f -s '${single_or_paired.input_mate2}' ${read2} && |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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39 #else if str($single_or_paired.single_or_paired_opts) == 'paired_collection': |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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40 #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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41 #set read1 = "input_f.fastq.gz" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
diff
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42 #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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43 #set read1 = "input_f.fastq.bz2" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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44 #else: |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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45 #set read1 = "input_f.fastq" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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46 #end if |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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47 ln -s '${single_or_paired.input_mate1.forward}' ${read1} && |
3
a6ea26c1f225
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
iuc
parents:
2
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48 |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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49 #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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50 #set read2 = "input_r.fastq.gz" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
diff
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51 #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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52 #set read2 = "input_r.fastq.bz2" |
3
a6ea26c1f225
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
iuc
parents:
2
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53 #else: |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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54 #set read2 = "input_r.fastq" |
3
a6ea26c1f225
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
iuc
parents:
2
diff
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55 #end if |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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56 ln -s '${single_or_paired.input_mate1.reverse}' ${read2} && |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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57 #else: |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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58 #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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59 #set read1 = "input_f.fastq.gz" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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60 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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61 #set read1 = "input_f.fastq.bz2" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
4
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62 #else: |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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63 #set read1 = "input_f.fastq" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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64 #end if |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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65 ln -f -s '${single_or_paired.input_singles}' ${read1} && |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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66 #end if |
3
a6ea26c1f225
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
iuc
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67 |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
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68 bwameth.py |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
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69 -t "\${GALAXY_SLOTS:-4}" |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
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70 --reference '${index}' |
0
f7094efef903
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
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71 |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
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72 #if str($readGroup).strip(): |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
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73 --read-group '${readGroup}' |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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74 #end if |
0
f7094efef903
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
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75 |
5
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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76 #if $single_or_paired.single_or_paired_opts == 'single': |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
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77 $read1 |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents:
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78 #else: |
29bdbc353f20
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
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79 $read1 $read2 |
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80 #end if |
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81 | samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o output.bam |
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82 |
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83 ]]></command> |
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84 <inputs> |
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85 <conditional name="referenceSource"> |
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86 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> |
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87 <option value="history" selected="True">Use one from the history</option> |
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88 <option value="indexed">Use a built-in index</option> |
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89 </param> |
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90 <when value="history"> |
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91 <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format" /> |
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92 </when> |
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93 <when value="indexed"> |
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94 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin"> |
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95 <options from_data_table="bwameth_indexes"> |
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96 <filter type="sort_by" column="2"/> |
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97 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
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98 </options> |
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99 </param> |
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100 </when> |
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101 </conditional> |
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102 |
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103 <conditional name="single_or_paired"> |
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104 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> |
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105 <option value="single">Single-end</option> |
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106 <option value="paired">Paired-end</option> |
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107 <option value="paired_collection">Paired-end Dataset Collection</option> |
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108 </param> |
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109 <when value="single"> |
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110 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file." /> |
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111 </when> |
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112 <when value="paired"> |
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113 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file." /> |
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114 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file." /> |
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115 </when> |
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116 <when value="paired_collection"> |
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117 <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." /> |
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118 </when> |
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119 </conditional> |
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120 <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'"> |
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121 <sanitizer sanitize="False"/> |
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122 </param> |
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123 </inputs> |
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124 <outputs> |
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125 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" /> |
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126 </outputs> |
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127 <tests> |
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128 <test> |
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129 <conditional name="referenceSource"> |
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130 <param name="source" value="history" /> |
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131 </conditional> |
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132 <param name="reference" value="ref.fa.gz" /> |
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133 <param name="single_or_paired_opts" value="paired" /> |
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134 <param name="input_mate1" value="t_R1.fastq.gz"/> |
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135 <param name="input_mate2" value="t_R2.fastq.gz"/> |
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136 <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff--> |
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137 </test> |
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138 <test> |
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139 <conditional name="referenceSource"> |
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140 <param name="source" value="history" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 8d6c5d539aa6689006776c1f6b2be9067bcf9d23"
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141 </conditional> |
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142 <param name="reference" value="ref.fa.gz" /> |
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143 <param name="single_or_paired_opts" value="paired_collection" /> |
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144 <param name="input_mate1"> |
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145 <collection type="paired"> |
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146 <element name="forward" value="t_R1.fastq.gz"/> |
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147 <element name="reverse" value="t_R2.fastq.gz"/> |
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148 </collection> |
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149 </param> |
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150 <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff--> |
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151 </test> |
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152 </tests> |
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153 <help><![CDATA[ |
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154 |
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155 **What it does** |
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156 |
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157 BWA-meth performs the alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. This methodology is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool. |
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158 ]]></help> |
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159 <citations> |
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160 <citation type="bibtex">@misc{1401.1129, |
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161 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz}, |
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162 Title = {Fast and accurate alignment of long bisulfite-seq reads}, |
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163 Year = {2014}, |
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164 Eprint = {arXiv:1401.1129}, |
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165 }</citation> |
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166 </citations> |
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167 </tool> |