Mercurial > repos > bgruening > bismark
annotate bismark_bowtie2_wrapper.xml @ 19:359f8b60d316 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
| author | bgruening |
|---|---|
| date | Fri, 04 Oct 2019 07:54:51 -0400 |
| parents | aa9bf0f29a9f |
| children | 120b7b35e442 |
| rev | line source |
|---|---|
|
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy4" profile="18.01"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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2 <description>Bisulfite reads mapper</description> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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3 <requirements> |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
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diff
changeset
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4 <requirement type="package" version="0.22.1">bismark</requirement> |
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8
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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5 <requirement type="package" version="1.8">samtools</requirement> |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
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diff
changeset
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6 <requirement type="package" version="2.3.5">bowtie2</requirement> |
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8
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
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7 </requirements> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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8 <command><![CDATA[ |
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b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
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9 #import re |
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b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
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10 |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
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11 #if $singlePaired.sPaired == "single": |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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12 #if $singlePaired.input_singles.ext == "fasta": |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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13 #set read1 = 'input_1.fa' |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: |
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19
359f8b60d316
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
bgruening
parents:
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changeset
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15 #if $params.settingsType == "custom" and $params.pbat == "--pbat" |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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diff
changeset
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16 #set read1 = 'input_1.fq' |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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17 #else |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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diff
changeset
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18 #set read1 = 'input_1.fq.gz' |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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19 #end if |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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20 #else |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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21 #set read1 = 'input_1.fq' |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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22 #end if |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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23 |
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19
359f8b60d316
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
bgruening
parents:
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diff
changeset
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24 #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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25 zcat '${singlePaired.input_singles}' > '${read1}' && |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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26 #else |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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27 ln -s '${singlePaired.input_singles}' '${read1}' && |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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28 #end if |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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29 #else: |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
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changeset
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30 #set $mate1 = list() |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
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changeset
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31 #set $mate2 = list() |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
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changeset
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32 #for $mate_pair in $singlePaired.mate_list |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
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changeset
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33 |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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34 #if $mate_pair.input_mate1.ext == "fasta": |
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0b656f8c5637
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
bgruening
parents:
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changeset
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35 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa' |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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36 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: |
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19
359f8b60d316
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
bgruening
parents:
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changeset
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37 #if $params.settingsType == "custom" and $params.pbat == "--pbat" |
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17
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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38 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
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39 #else |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
16
diff
changeset
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40 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz' |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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41 #end if |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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42 #else |
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15
0b656f8c5637
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
bgruening
parents:
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diff
changeset
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43 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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44 #end if |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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45 |
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19
359f8b60d316
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
bgruening
parents:
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46 #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: |
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17
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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47 zcat '${mate_pair.input_mate1}' > '${read1}' && |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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48 #else |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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49 ln -s '${mate_pair.input_mate1}' '${read1}' && |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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50 #end if |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
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51 |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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52 #if $mate_pair.input_mate2.ext == "fasta": |
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15
0b656f8c5637
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
bgruening
parents:
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changeset
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53 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa' |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
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54 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: |
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19
359f8b60d316
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
bgruening
parents:
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55 #if $params.settingsType == "custom" and $params.pbat == "--pbat" |
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17
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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56 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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57 #else |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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58 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz' |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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59 #end if |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
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60 #else |
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15
0b656f8c5637
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
bgruening
parents:
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61 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
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62 #end if |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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63 |
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19
359f8b60d316
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
bgruening
parents:
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64 #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: |
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17
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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65 zcat '${mate_pair.input_mate2}' > '${read2}' && |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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66 #else |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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67 ln -s '${mate_pair.input_mate2}' '${read2}' && |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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68 #end if |
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14
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
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69 |
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b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
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70 $mate1.append( str($read1) ) |
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b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
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71 $mate2.append( str($read2) ) |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
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72 #end for |
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f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
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73 #end if |
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74 |
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8
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75 python '$__tool_directory__/bismark_wrapper.py' |
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76 |
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77 ## Change this to accommodate the number of threads you have available. |
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78 --num-threads "\${GALAXY_SLOTS:-4}" |
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79 |
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80 ## |
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81 ## Bismark Genome Preparation, if desired. |
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82 ## |
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83 |
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84 ## Handle reference file. |
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85 #if $refGenomeSource.genomeSource == "built_in_fasta": |
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86 --own-file '${refGenomeSource.built_in_fasta.fields.path}' |
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87 #else if $refGenomeSource.genomeSource == "history": |
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88 --own-file '$refGenomeSource["own_file"]' |
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89 #else: |
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90 --indexes-path '${refGenomeSource.built_in_indexes.fields.path}' |
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91 #end if |
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92 |
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93 ## |
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94 ## Input parameters |
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95 ## |
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96 |
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97 #if $singlePaired.sPaired == "single": |
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98 --single-paired '${read1}' |
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99 |
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100 #if $singlePaired.input_singles.ext in ["fastq", "fastq.gz", "fastqillumina"]: |
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101 --phred64-quals |
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102 --fastq |
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103 #elif $singlePaired.input_singles.ext in ["fastqsanger", "fastqsanger.gz"]: |
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104 --fastq |
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105 #elif $singlePaired.input_singles.ext == "fasta": |
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106 --fasta |
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107 #end if |
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108 #else: |
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109 --mate-paired |
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110 |
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111 --mate1 #echo ','.join($mate1) |
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112 --mate2 #echo ','.join($mate2) |
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113 |
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114 #for $mate_pair in $singlePaired.mate_list: |
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115 #if $mate_pair.input_mate1.ext == "fastqillumina": |
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116 --phred64-quals |
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117 --fastq |
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118 #elif $mate_pair.input_mate1.ext in "fastqsanger,fastqsanger.gz": |
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119 --fastq |
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120 #elif $mate_pair.input_mate1.ext == "fasta": |
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121 --fasta |
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122 #end if |
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123 #break |
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124 #end for |
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125 |
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126 -I $singlePaired.minInsert |
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127 -X $singlePaired.maxInsert |
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128 #end if |
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129 |
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130 #if $sort_bam: |
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131 --sort-bam |
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132 #end if |
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133 |
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134 ## for now hardcode the value for the required memory per thread in --best mode |
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135 --chunkmbs 512 |
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136 |
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137 |
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138 #if $params.settingsType == "custom": |
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139 |
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140 ## default 20 |
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141 --seed-len $params.seed_len |
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142 ## default 0 |
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143 --seed-mismatches $params.seed_mismatches |
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144 ## default 15 |
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145 --seed-extention-attempts $params.seed_extention_attempts |
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146 ## default 2 |
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147 --max-reseed $params.max_reseed |
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148 |
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149 ## default unlimited |
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150 #if $params.qupto != 0: |
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151 --qupto $params.qupto |
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152 #end if |
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153 #if $params.skip_reads != 0: |
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154 --skip-reads $params.skip_reads |
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155 #end if |
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156 |
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16
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
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157 #if $params.score_min != "": |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
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158 --score-min '${params.score_min}' |
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a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
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159 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
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160 |
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161 ## if set, disable the original behaviour |
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162 $params.no_mixed |
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163 ## if set, disable the original behaviour |
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164 $params.no_discordant |
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165 |
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166 $params.non_directional |
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167 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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168 $params.pbat |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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169 |
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170 #if $params.bismark_stdout: |
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171 --stdout '$output_stdout' |
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172 #end if |
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173 |
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174 #if $params.isReportOutput: |
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175 --output-report-file '$report_file' |
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176 #end if |
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177 |
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178 #else: |
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179 --output-report-file '$report_file' |
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180 #end if |
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181 |
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182 ## |
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183 ## Output parameters. |
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184 ## |
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185 --output '$output' |
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186 ##$suppress_header |
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187 |
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188 #if str( $singlePaired.sPaired ) == "single" |
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189 #if $output_unmapped_reads_l |
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190 --output-unmapped-reads '$output_unmapped_reads_l' |
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191 #end if |
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192 #if $output_suppressed_reads_l |
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193 --output-suppressed-reads '$output_suppressed_reads_l' |
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194 #end if |
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195 #else |
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196 #if $output_unmapped_reads_l and $output_unmapped_reads_r |
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197 --output-unmapped-reads-l '$output_unmapped_reads_l' |
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198 --output-unmapped-reads-r '$output_unmapped_reads_r' |
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199 #end if |
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200 #if $output_suppressed_reads_l and $output_suppressed_reads_l |
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201 --output-suppressed-reads-l '$output_suppressed_reads_l' |
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202 --output-suppressed-reads-r '$output_suppressed_reads_r' |
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203 #end if |
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204 #end if |
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205 |
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206 ]]> |
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207 </command> |
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208 <inputs> |
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209 <conditional name="refGenomeSource"> |
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210 <param name="genomeSource" type="select" |
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211 label="Will you select a reference genome from your history or use a built-in index?" |
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212 help="Built-ins were indexed using default options"> |
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213 <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option> |
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214 <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option> |
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215 <option value="history">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option> |
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216 </param> |
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217 <when value="built_in_indexes"> |
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218 <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)" |
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219 help="If your genome of interest is not listed, contact your Galaxy admin"> |
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220 <options from_data_table="bismark_indexes"> |
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221 <filter type="sort_by" column="name"/> |
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222 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
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223 </options> |
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224 </param> |
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225 </when> |
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226 <when value="built_in_fasta"> |
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227 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)"> |
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228 <options from_data_table="all_fasta"> |
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229 <filter type="sort_by" column="name"/> |
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230 <validator type="no_options" |
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231 message="No genomes in fasta are available for the selected input dataset"/> |
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232 </options> |
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233 </param> |
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234 </when> |
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235 <when value="history"> |
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236 <param name="own_file" type="data" format="fasta" label="Select the reference genome"/> |
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237 </when> |
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238 </conditional> |
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239 |
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240 <!-- Input Parameters --> |
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241 <conditional name="singlePaired"> |
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242 <param name="sPaired" type="select" label="Is this library mate-paired?"> |
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243 <option value="single">Single-end</option> |
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244 <option value="paired">Paired-end</option> |
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245 </param> |
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246 <when value="single"> |
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247 <param name="input_singles" type="data" |
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248 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="FASTQ/FASTA file" |
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249 help="FASTQ or FASTA files."/> |
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250 </when> |
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251 <when value="paired"> |
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252 <repeat name="mate_list" title="Paired End Pairs" min="1"> |
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253 <param name="input_mate1" type="data" |
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254 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 1" |
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255 help="FASTQ or FASTA files."/> |
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256 <param name="input_mate2" type="data" |
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257 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 2" |
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258 help="FASTQ or FASTA files."/> |
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259 </repeat> |
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260 <param name="minInsert" type="integer" value="0" |
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261 label="Minimum insert size for valid paired-end alignments"/> |
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262 <param name="maxInsert" type="integer" value="500" |
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263 label="Maximum insert size for valid paired-end alignments"/> |
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264 </when> |
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265 </conditional> |
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266 |
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267 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False" |
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268 label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/> |
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269 |
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270 <conditional name="params"> |
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271 <param name="settingsType" type="select" label="Bismark settings to use" |
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272 help="You can use the default settings or set custom values for any of Bismark's parameters."> |
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273 <option value="default">Use Defaults</option> |
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274 <option value="custom">Full parameter list</option> |
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275 </param> |
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276 <!-- Full/advanced params. --> |
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277 <when value="default"></when> |
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278 <when value="custom"> |
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279 <!-- -N --> |
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280 <param name="seed_mismatches" type="integer" value="0" |
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281 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/> |
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282 <!-- -L --> |
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283 <param name="seed_len" type="integer" value="20" |
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284 label="Length of the seed substrings to align during multiseed alignment"/> |
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285 |
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286 <!-- -D --> |
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287 <param name="seed_extention_attempts" type="integer" value="15" |
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288 label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/> |
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289 <!-- -R --> |
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290 <param name="max_reseed" type="integer" value="2" |
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291 label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds"/> |
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292 |
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293 <param name="qupto" type="integer" value="0" |
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294 label="Only aligns the first N reads or read pairs from the input" |
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295 help="Default is 0 and means 'no-limit'."/> |
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296 <param name="skip_reads" type="integer" value="0" |
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297 label="Skip (i.e. do not align) the first N reads or read pairs from the input"/> |
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298 |
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299 <param argument="--score-min" name="score_min" type="text" value="" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="This is a function of read length. For instance, specifying `L,0,-0.2` sets the minimum-score function `f` to `f(x) = 0 + -0.2 * x`, where `x` is the read length."/> |
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300 |
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301 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false" |
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302 label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)" |
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303 help=""/> |
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304 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false" |
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305 label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates (only for paired-end reads" |
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306 help=""/> |
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307 |
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308 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" |
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309 label="Write ambiguous reads to an extra output file" |
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310 help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely."/> |
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311 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" |
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312 label="Write all reads that could not be aligned to a file"/> |
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313 <!-- output Options --> |
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314 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" |
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315 label="Write the bismark output and summary information to an extra file"/> |
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316 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" |
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317 label="Offer all report files concatenated in one file (Mapping Report)"/> |
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318 <param argument="--non-directional" name="non_directional" type="boolean" |
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319 truevalue="--non-directional" falsevalue="" checked="false" |
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320 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/> |
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321 <param argument="--pbat" name="pbat" type="boolean" |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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322 truevalue="--pbat" falsevalue="" checked="false" |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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323 label="Treat input data as PBAT-Seq libraries" |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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324 help="Use this option only if you are certain that your libraries were constructed following a PBAT protocol. If you don't know what PBAT-Seq is you should not specify this option." /> |
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aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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325 |
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8
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326 |
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327 <!--end output options --> |
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328 </when> <!-- full --> |
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329 </conditional> <!-- params --> |
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9bfe38410155
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330 <!-- |
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331 <param name="suppress_header" type="boolean" truevalue="..suppress-header" falsevalue="" checked="false" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default." /> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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332 --> |
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9bfe38410155
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333 </inputs> |
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9bfe38410155
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334 |
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9bfe38410155
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335 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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336 <outputs> |
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9bfe38410155
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337 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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338 <filter> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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339 (( |
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340 params['settingsType'] == "default" or |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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341 ( params['settingsType'] == "custom" and |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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342 params['isReportOutput'] is True ) |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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343 )) |
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344 </filter> |
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345 </data> |
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9bfe38410155
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346 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary"> |
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9bfe38410155
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347 <filter> |
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9bfe38410155
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348 (( |
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349 params['settingsType'] == "custom" and |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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350 params['bismark_stdout'] is True |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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351 )) |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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352 </filter> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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353 </data> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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354 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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|
355 <data format="qname_input_sorted.bam" name="output" label="${tool.name} on ${on_string}: mapped reads"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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356 <actions> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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357 <conditional name="refGenomeSource.genomeSource"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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358 <when value="built_in_indexes"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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359 <action type="metadata" name="dbkey"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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360 <option type="from_data_table" name="bismark_indexes" column="1" offset="0"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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361 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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362 <filter type="param_value" ref="refGenomeSource.built_in_indexes" column="0"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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363 </option> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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364 </action> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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365 </when> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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366 <when value="generate_indexes"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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367 <action type="metadata" name="dbkey"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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368 <option type="from_data_table" name="all_fasta" column="1" offset="0"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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369 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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370 <filter type="param_value" ref="refGenomeSource.generate_indexes" column="0"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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371 </option> |
|
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372 </action> |
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373 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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374 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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375 </actions> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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376 <change_format> |
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377 <when input="sort_bam" value="true" format="bam"/> |
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378 <when input="sort_bam" value="false" format="qname_input_sorted.bam"/> |
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379 </change_format> |
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380 </data> |
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381 |
|
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382 <data format="fastq" name="output_suppressed_reads_l" |
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383 label="${tool.name} on ${on_string}: suppressed reads (L)"> |
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384 <filter> |
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385 (( |
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386 params['settingsType'] == "custom" and |
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387 params['suppressed_read_file'] is True |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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388 )) |
|
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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389 </filter> |
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390 <actions> |
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391 <conditional name="singlePaired.sPaired"> |
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392 <when value="single"> |
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393 <action type="format"> |
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394 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/> |
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395 </action> |
|
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396 </when> |
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397 </conditional> |
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398 </actions> |
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|
399 </data> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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400 |
|
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401 <data format="fastq" name="output_suppressed_reads_r" |
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402 label="${tool.name} on ${on_string}: suppressed reads (R)"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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|
403 <filter> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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|
404 (( |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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405 singlePaired['sPaired'] == "paired" and |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff
changeset
|
406 params['settingsType'] == "custom" and |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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407 params['suppressed_read_file'] is True |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
408 )) |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
409 </filter> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
410 <actions> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
|
411 <conditional name="singlePaired.sPaired"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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412 <when value="single"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
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413 <action type="format"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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414 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
415 </action> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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416 </when> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
417 <!--when value="paired"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
418 <action type="format"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
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419 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
420 </action> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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421 </when--> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
422 </conditional> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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423 </actions> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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424 </data> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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425 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
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426 <!-- Outout unmapped reads --> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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427 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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428 <filter> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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429 (( |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
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430 params['settingsType'] == "custom" and |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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431 params['unmapped_read_file'] is True |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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432 )) |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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433 </filter> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
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434 <actions> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
435 <conditional name="singlePaired.sPaired"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
436 <when value="single"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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437 <action type="format"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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438 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
439 </action> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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440 </when> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
441 <!--when value="paired"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
442 <action type="format"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
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443 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
444 </action> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
445 </when--> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
446 </conditional> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
447 </actions> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
448 </data> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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449 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
450 <filter> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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451 (( |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
452 singlePaired['sPaired'] == "paired" and |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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453 params['settingsType'] == "custom" and |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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454 params['unmapped_read_file'] is True |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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455 )) |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
456 </filter> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
457 <actions> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
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458 <conditional name="singlePaired.sPaired"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
459 <when value="single"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
460 <action type="format"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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461 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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462 </action> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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463 </when> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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464 <!--when value="paired"> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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465 <action type="format"> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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466 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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467 </action> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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468 </when--> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
469 </conditional> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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470 </actions> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
471 </data> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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472 </outputs> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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473 <tests> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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474 <test> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
475 <param name="genomeSource" value="history"/> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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476 <param name="own_file" value="mm10.tiny.fa.gz" /> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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477 <param name="sPaired" value="single"/> |
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13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
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diff
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478 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/> |
|
8
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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479 <param name="sort_bam" value="false"/> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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480 <param name="settingsType" value="custom"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
481 <param name="suppressed_read_file" value="true"/> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
482 <param name="unmapped_read_file" value="true"/> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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483 <param name="bismark_stdout" value="true"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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484 <param name="isReportOutput" value="true"/> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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485 |
|
15
0b656f8c5637
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
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diff
changeset
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486 <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="94"> |
|
8
9bfe38410155
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parents:
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changeset
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487 <assert_contents> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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488 <has_text text="Sequences analysed in total:" /> |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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489 <has_text text="44115" /> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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490 <has_text text="Mapping efficiency:" /> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
491 <has_text text="1.3%" /> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
492 <has_text text="Bismark run complete" /> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
493 </assert_contents> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
494 </output> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
495 <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
496 <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
497 </test> |
|
13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
498 <test> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
499 <param name="genomeSource" value="history"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
500 <param name="own_file" value="mm10.tiny.fa.gz" /> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
501 <param name="sPaired" value="single"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
502 <param name="input_singles" value="input1.fq" ftype="fastqsanger"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
503 <param name="sort_bam" value="false"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
504 <param name="settingsType" value="custom"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
505 <param name="suppressed_read_file" value="true"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
506 <param name="unmapped_read_file" value="true"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
507 <param name="bismark_stdout" value="true"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
508 <param name="isReportOutput" value="true"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
509 |
|
15
0b656f8c5637
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
bgruening
parents:
14
diff
changeset
|
510 <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="94"> |
|
13
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
511 <assert_contents> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
512 <has_text text="Sequences analysed in total:" /> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
513 <has_text text="1000" /> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
514 <has_text text="Mapping efficiency:" /> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
515 <has_text text="0.8%" /> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
516 <has_text text="Bismark run complete" /> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
517 </assert_contents> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
518 </output> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
519 <output name="report_file" file="mapping_report_short.txt" ftype="txt" lines_diff="6"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
520 <output name="output" file="mapped_reads_short.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> |
|
f211753166bd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents:
11
diff
changeset
|
521 </test> |
|
14
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
522 <test> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
523 <param name="genomeSource" value="history"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
524 <param name="own_file" value="mm10.tiny.fa.gz" /> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
525 <param name="sPaired" value="paired"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
526 <repeat name="mate_list"> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
527 <param name="input_mate1" value="input1.fq" ftype="fastqsanger"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
528 <param name="input_mate2" value="input1.fq" ftype="fastqsanger"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
529 </repeat> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
530 <param name="sort_bam" value="false"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
531 <param name="settingsType" value="custom"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
532 <param name="suppressed_read_file" value="true"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
533 <param name="unmapped_read_file" value="true"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
534 <param name="bismark_stdout" value="true"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
535 <param name="isReportOutput" value="true"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
536 |
|
15
0b656f8c5637
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
bgruening
parents:
14
diff
changeset
|
537 <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="94"> |
|
14
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
538 <assert_contents> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
539 <has_text text="Sequence pairs analysed in total:" /> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
540 <has_text text="1000" /> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
541 <has_text text="Mapping efficiency:" /> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
542 <has_text text="0.0%" /> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
543 <has_text text="Bismark run complete" /> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
544 </assert_contents> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
545 </output> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
546 <output name="report_file" file="mapping_report_mate.txt" ftype="txt" lines_diff="6"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
547 <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> |
|
b6aa3b6ba129
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
13
diff
changeset
|
548 </test> |
|
16
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
549 <test> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
550 <param name="genomeSource" value="history"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
551 <param name="own_file" value="mm10.tiny.fa.gz" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
552 <param name="sPaired" value="single"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
553 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
554 <param name="sort_bam" value="false"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
555 <param name="settingsType" value="custom"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
556 <param name="suppressed_read_file" value="true"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
557 <param name="unmapped_read_file" value="true"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
558 <param name="bismark_stdout" value="true"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
559 <param name="isReportOutput" value="true"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
560 <conditional name="params"> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
561 <param name="settingsType" value="custom" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
562 <param name="score_min" value="L,0,-0.8" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
563 </conditional> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
564 |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
565 <output name="output_stdout" file="summary_custom.txt" ftype="txt" lines_diff="94"> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
566 <assert_contents> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
15
diff
changeset
|
567 <has_text text="Sequences analysed in total:" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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568 <has_text text="44115" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
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diff
changeset
|
569 <has_text text="Mapping efficiency:" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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|
570 <has_text text="4.5%" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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diff
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|
571 <has_text text="Bismark run complete" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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|
572 </assert_contents> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
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diff
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|
573 </output> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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|
574 <output name="report_file" file="mapping_report_custom.txt" ftype="txt" lines_diff="6"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
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|
575 <output name="output" file="mapped_reads_custom.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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diff
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|
576 |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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|
577 <assert_command> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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578 <has_text text="--score-min 'L,0,-0.8'" /> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents:
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|
579 </assert_command> |
|
a4504327c890
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
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580 </test> |
|
17
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
581 <test> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
582 <param name="genomeSource" value="history"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
583 <param name="own_file" value="mm10.tiny.fa.gz" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
584 <param name="sPaired" value="single"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
585 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
|
586 <param name="sort_bam" value="false"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
587 <param name="settingsType" value="custom"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
588 <param name="suppressed_read_file" value="true"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
589 <param name="unmapped_read_file" value="true"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
590 <param name="bismark_stdout" value="true"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
591 <param name="isReportOutput" value="true"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
592 <conditional name="params"> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
593 <param name="settingsType" value="custom" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
594 <param name="pbat" value="true" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
595 </conditional> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
|
596 |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
16
diff
changeset
|
597 <output name="output_stdout" file="summary_pbat.txt" ftype="txt" lines_diff="94"> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
|
598 <assert_contents> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
599 <has_text text="Sequences analysed in total:" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
600 <has_text text="44115" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
|
601 <has_text text="Mapping efficiency:" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
16
diff
changeset
|
602 <has_text text="0.0%" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
603 <has_text text="Bismark run complete" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
604 </assert_contents> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
605 </output> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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changeset
|
606 <output name="report_file" file="mapping_report_pbat.txt" ftype="txt" lines_diff="6"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
607 <output name="output" file="mapped_reads_pbat.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
608 |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
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|
609 <assert_command> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
610 <has_text text="--pbat" /> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
611 </assert_command> |
|
aa9bf0f29a9f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
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|
612 </test> |
|
8
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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|
613 </tests> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
614 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
615 <help> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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|
616 <![CDATA[ |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
617 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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|
618 **What it does** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
619 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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|
620 | Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the reads to a specified bisulfite genome. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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|
621 | Sequence reads are transformed into a bisulfite converted forward strand version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand). |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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622 | Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the forward strand, by doing this alignments will produce the same positions). |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
623 | These instances of Bowtie 2 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original sequence from the genome and determine if there were any protected C's present or not. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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624 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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625 | As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be re-enabled by using non_directional mode. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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626 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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627 | It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
|
628 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
|
629 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
630 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
|
631 ---- |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
632 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
633 **Know what you are doing** |
|
9bfe38410155
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changeset
|
634 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
635 .. class:: warningmark |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
636 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
637 | There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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638 | In other words = running this tool with default parameters will probably not give you meaningful results. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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|
639 | A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
640 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
641 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
|
642 .. class:: warningmark |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
643 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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644 | Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff
changeset
|
645 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff
changeset
|
646 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
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9bfe38410155
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parents:
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changeset
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647 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
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648 ---- |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff
changeset
|
649 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
650 **Input formats** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
651 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
652 | Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
653 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
654 ---- |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
655 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
656 **A Note on Built-in Reference Genomes** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
657 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
658 | The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
659 | When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
660 | The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
661 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
662 ---- |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
663 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
664 **Outputs** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
665 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
666 * The final output of Bismark is in SAM format by default, and has the following columns:: |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
667 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
668 Column Description |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
669 -------- -------------------------------------------------------- |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
670 1 QNAME seq-ID |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
671 2 FLAG this flag tries to take the strand a bisulfite read |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
672 originated from into account |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
673 (this is different from ordinary DNA alignment flags!) |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
674 3 RNAME chromosome |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
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675 4 POS start position |
|
9bfe38410155
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parents:
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changeset
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676 5 MAPQ always 255 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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677 6 CIGAR extended CIGAR string |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
678 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME) |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
679 8 MPOS 1-based Mate POSition |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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680 9 ISIZE Inferred insert SIZE |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
681 10 SEQ query SEQuence on the same strand as the reference |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
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682 11 QUAL Phred33 scale |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
683 12 NM-tag edit distance to the reference) |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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684 13 XX-tag base-by-base mismatches to the reference. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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685 This does not include indels. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff
changeset
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686 14 XM-tag methylation call string |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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687 15 XR-tag read conversion state for the alignment |
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9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff
changeset
|
688 16 XG-tag genome conversion state for the alignment |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
689 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
690 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
691 | Each read of paired-end alignments is written out in a separate line in the above format. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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692 | |
|
9bfe38410155
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changeset
|
693 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
694 * It looks like this (scroll sideways to see the entire example):: |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
695 |
|
9bfe38410155
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changeset
|
696 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT |
|
9bfe38410155
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697 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
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698 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
699 |
|
9bfe38410155
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700 ---- |
|
9bfe38410155
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parents:
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changeset
|
701 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
702 **Note on Bismark settings** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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changeset
|
703 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
704 | All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
705 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
706 ---- |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
707 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
708 **Bismark settings** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
709 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
710 * **If Paired-End Reads** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
711 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
712 * **Minimum insert size for valid paired-end alignments** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
713 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
714 | The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. Default: 0. |
|
9bfe38410155
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bgruening
parents:
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changeset
|
715 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
716 | Alignment option *-I/--minins <INT>* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff
changeset
|
717 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
718 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
719 * **Maximum insert size for valid paired-end alignments** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
720 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
721 | The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. Default: 500. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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changeset
|
722 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
723 | Alignment option *-X/--maxins <INT>* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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changeset
|
724 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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changeset
|
725 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
726 * **Number of mismatches to be allowed in a seed alignment during multiseed alignment** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
727 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
728 | Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for Bowtie 1 see -n). |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
729 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
730 | Bowtie 2 Specific option *-N <INT>* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
731 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
732 * **Length of the seed substrings to align during multiseed alignment** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
733 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
734 | Sets the length of the seed substrings to align during multiseed alignment. Smaller values make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is used by default, which sets -L to 20. This option is only available for Bowtie 2 (for Bowtie 1 see -l). |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
735 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
736 | Bowtie 2 Specific option *-L <INT>* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
737 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
738 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
739 * **How many consecutive seed extension attempts can fail before Bowtie 2 moves on** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
740 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
741 | Up to <int> consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using the alignments found so far. A seed extension "fails" if it does not yield a new best or a new second-best alignment. Default: 15. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
742 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
743 | Bowtie 2 Effort option *-D <INT>* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
744 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
745 * **Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
746 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
747 | <int> is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds. 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. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
748 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
749 | Bowtie 2 Effort option *-R <INT>* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
750 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
751 * **Only aligns the first N reads or read pairs from the input** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
752 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
753 | Only aligns the first <int> reads or read pairs from the input. Default: no limit. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
754 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
755 | Input option *-u/--upto <INT>* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
756 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
757 * **Skip (i.e. do not align) the first N reads or read pairs from the input** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
758 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
759 | Input option *-s/--skip* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
760 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
761 * **Disable looking for discordant alignments if it cannot find any concordant alignments** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
762 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
763 | Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior and it is on by default. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
764 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
765 | Bowtie 2 Paired-End option *--no-discordant* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
766 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
767 * **Disable Bowtie 2's behaviour to try to find alignments for the individual mates** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
768 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
769 | This option disables Bowtie 2's behavior to try to find alignments for the individual mates if it cannot find a concordant or discordant alignment for a pair. This option is invariable and on by default. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
770 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
771 | Bowtie 2 Paired-End option *--no-mixed* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
772 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
773 * **Write ambiguous reads to an extra output file** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
774 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
775 | Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely to a file in the output directory. Written reads will appear as they did in the input, without any of the translation of quality values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and _ambiguous_reads_2.txt. These reads are not written to the file specified with --un. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
776 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
777 | Output option *--ambiguous* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
778 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
779 * **Write all reads that could not be aligned to a file** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
780 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
781 | Write all reads that could not be aligned to a file in the output directory. Written reads will appear as they did in the input, without any translation of quality values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping) are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well. |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
782 | |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
783 | Output option *-un/--unmapped* |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
784 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
785 * **Offer all report files concatenated in one file** |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
786 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
787 | Prints out a Bismark mapping report |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
788 |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
789 ]]> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
790 </help> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
791 <citations> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
792 <citation type="doi">10.1093/bioinformatics/btr167</citation> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
793 </citations> |
|
9bfe38410155
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff
changeset
|
794 </tool> |